title: Transcriptome analysis of aflatoxin B1 (AFB1) induced hepatocellular carcinoma (HCC) and AFB1 resistant liver sample from rats

status: Public on Jan 20 2016

first: Jiejun

last: Shi

address: No.1239, Siping Road

institute: Tongji University

summary: Applied de novo assembly, both protein coding and non-coding RNAs were profiled in AFB1 induced HCC and AFB1 resistant liver sample. Compared with normal liver, the perturbation on transcriptome was revealed in multiple aspects, implying the potential mechanism of toxic resistance.

overall_design: All rats were randomly divided into control and treated groups according to their weight. Then AFB1 was injected intraperitoneally to treated group in customized schedule. Biopsy was applied every 10 weeks on both groups. Tissues from rats died of HCC were reserved. All rats were sacrificed at 70th week. According to whether tumor formed, liver tissues from animals in treated group were further divided into AFB1 induced tumor sample and AFB1 resistant sample. Both samples were stored for later transcriptome analysis, as well as the normal sample from control group. RNA profiles of all 3 samples were generated by deep sequencing, using Illumina HiSeq2000 platform.

first: Cizhong


title: Comparative metabolic and transcriptional analysis of a doubled diploid and its diploid citrus rootstock (C. junos cv. Ziyang xiangcheng) suggests its potential value for stress resistance improvement

status: Public on Jan 29 2016

city: Wuhan

first: Fengquan

last: Tan

address: Hongshan

country: China

institute: HZAU

type: Expression profiling by high throughput sequencing

summary: To investigate global genome expression changes caused by tetraploidization, we  compared, by RNA-Seq analysis, the nuclear gene expression profiles of mature leaves of the diploid citrus rootstock and its doubled diploid. A total of 212 genes were differentially expressed between the diploid and doubled dipoid. In biological process category, DEGs were found to be highly related to stress-response functions, such as response to salt stress, to water, and to abscisic acid. In molecular function category, only two terms were overrepresented, namely, inorganic anion transmembrane transporter activity, inorganic phosphate transmembrane transporter activity.

overall_design: Total four sample pools (two independent biological replicates of the diploid and doubled diploid mature leaves)

first: Wenwu

last: Guo


title: The insect midgut is not restful during the larva-to-larva molting stage

status: Public on Feb 01 2016

city: Shanghai

first: Bing

last: Yang

state: Shanghai

institute: SIBS，CAS

summary: IMolting, a special period during which the old cuticle is shed and a new one is produced, is crucial to insect development. During their life cycles, insects that undergo complete metamorphosis may experience several larva-to-larva moltings to become larger, followed by larva-to-pupa and pupa-to-adult moltings to become adults. During the larva-to-larva molting stage, insect larvae stop consuming food and become restful. Whether any changes occur within the molting midgut before ecdysis remains known.

overall_design: Total RNA from day 3 of 4th feeding, 4th molting and 5th feeding stages Bombyx midgut were used to generate target cDNA, and then hybridized to 48k Bombyx genome Array Genechips, representing about 23000 characterized genes

first: Erjun

last: Ling


title: Deciphering the importance of the palindromic architecture of the immunoglobulin heavy chain 3’ regulatory region.

status: Public on Feb 08 2016

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary: The IgH 3’ regulatory region (3’RR) controls class switch recombination (CSR) and somatic hypermutation (SHM) in B cells. The mouse 3’RR contains four enhancer elements with hs1,2 flanked by inverted repeated sequences and the center of a 25-kb palindrome bounded by two hs3 enhancer inverted copies (hs3a and hs3b). hs4 lies downstream of the palindrome. Evolution maintained in mammals this unique palindromic arrangement suggesting that it is functionally significant. We report that deconstructing the palindromic IgH 3’RR strongly impacts its function even when enhancers are preserved. CSR and IgH transcription appear poorly dependent from the 3’RR architecture and are more or less preserved provided 3’RR enhancers are present. By contrast, an “architectural effect” significantly lowers VH germline transcription, AID recruitment and SHM. In conclusion, this work indicates that the IgH 3’RR does not simply pile up enhancer units but also optimally expose them into a functional architecture of crucial importance.

overall_design: RNAseq analysis of B-cell splenocytes with (S=stimulated) or without (R=resting) LPS activation from wt, delta2leftPAL, and deltaIRIS mice.

first: Y

last: DENIZOT

first: V

last: MAGNONNE

first: K

last: LEBRIGAND

first: P

last: BARBRY


title: RNA-seq of human fibroblasts during replicative senescence

status: Public on Jan 18 2016

city: Jena

first: JenAge

last: Project

address: Beutenbergstr. 11

country: Germany

institute: Leibniz Institute for Age Research - Fritz Lipmann Institute

summary:
Senescent human fibroblasts were compared to young proliferating fibroblasts. Five different cell lines were compared. Illumina sequencing (HiSeq2000) was applied to generate 50bp single-end reads.

Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 48 samples: 3 biological replicates for each group: young proliferating and senescent BJ cells;  young proliferating and senescent Wi-38 cells;  young proliferating and senescent IMR-90 cells; 5 population doubling from young proliferating to senescent cell for HFF and MRC-5 cells

first: Shiva

last: Marthandan

first: Karolin

last: Klement

first: Steffen

last: Priebe

first: Marco

last: Groth

first: Matthias

last: Platzer

first: Peter

last: Hemmerich

first: Stephan

last: Diekmann


title: Autonomous extracellular matrix remodeling controls a progressive adaptation in muscle stem cell regenerative capacity during development

city: La Jolla

first: Francesca

last: Boscolo

state: CA

address: 9500 Gilman Drive

department: Reproductive Medicine

country: USA

institute: UCSD

summary: Muscle stem cells (MuSC) exhibit distinct behaviors during successive phases of developmental myogenesis. However, how their transition to adulthood is regulated is poorly understood. Here we show that fetal MuSC resist progenitor specification and exhibit altered division dynamics, intrinsic features that are progressively lost postnatally. Following transplantation, fetal MuSC more efficiently expand and contribute to muscle repair. Conversely, the efficiency of niche colonization increases in adulthood, indicating a balance between muscle growth and stem cell pool repopulation. Gene expression profiling identified several extracellular matrix (ECM) molecules preferentially expressed in fetal MuSC, including tenascin-C, fibronectin and collagen VI. Loss-of-function experiments confirmed their essential and stage-specific role in regulating MuSC function. Finally, fetal-derived paracrine factors were able to enhance adult MuSC regenerative potential. Together, these findings demonstrate that MuSC change the way in which they remodel their microenvironment to direct stem cell behavior in support of the unique demands of muscle development or repair.

overall_design: MuSCs were isolated through fluorescent-activate cell sorting usinf alpha7-integirn and CD34 as markers to identify the cell population. Total mRNA was then isolated, and samples at different developmental times were compared.

first: Matthew

middle: T

last: Tierney

first: Anastasia

last: Gromova

middle: B

last: Sesillo

first: David

last: Sala

first: Caroline

last: Spenle

first: Gertraud

last: Orend

first: Alessandra

last: Sacco


title: CRC cells_Aspirin treatment_48 hours_Rep8

status: Public on Jan 07 2016

first: Jianjun

last: Zhang

address: No.639, Zhizaoju road

institute: Shanghai Jiaotong University

summary:
To identify the lncRNA profiles of colorectal carcinoma cells treated with aspirin, we performed microarray analysis using primary cultured cancer cells obtained from 8 clinical CRC tissues.
After the CRC cells were treated with aspirin for 48 hours, 28 lncRNAs were statistically up-regulated more than 2-fold.

overall_design: We treated the primary cultured cancer cells obtained from 8 clinical CRC tissues with DMSO (negative control group_Rep8) and aspirin (Experiment group_Rep8).

first: Qidong

last: Zhu

first: Man

last: Li


title: p53 deficiency linked to BTG2 loss enhances metastatic potential by promoting tumor growth in primary and metastatic sites in PDX models of triple negative breast cancer

city: Houston

first: Emily

last: Powell

state: TX

address: 1901 East Road

institute: MD Anderson

summary: We performed differential expression analyses from RNA-seq data derived from isogenic p53 wild-type and p53-knockdown triple negative breast tumors

overall_design: patient-derived isogenic human tumor lines diffring only in p53 status were implanted into mouse mammary glands. RNA-Seq was performed on 4 p53-deficient and 3 p53 wild-type tumors.

first: Nipun

last: Mistry

first: Keith

middle: F

last: Decker

first: John

middle: R

last: Edwards

first: Han

last: Liang


title: Invariant TAD boundaries constrain cell type-specific looping interactions between promoters and distal elements around the CFTR locus.

city: Worcester

first: Bryan

last: Lajoie

state: MA

address: 368 Plantation St.

department: Program in Systems Biology

institute: UMMS

summary: Three-dimensional genome structure plays an important role in gene regulation.  Globally chromosomes are organized into active and inactive compartments, while at the gene level looping interactions connect promoters to regulatory elements.  Topologically Associating Domains (TADs), typically several hundred kilobases in size form an intermediate level of organization.  Major questions include how TADs are formed and what their relation is with looping interactions between genes and regulatory elements.  Here we performed a focused 5C analysis of a 2.8 Mb region on chromosome 7 surrounding CFTR in a panel of cell types.  We find that the same TAD boundaries are present in all cell types, indicating that TADs represent a universal chromosome architecture.  Further, we find that these TAD boundaries are present irrespective of expression and looping of genes located between them.  In contrast looping interactions between promoters and regulatory elements are cell-type specific and occur mostly within TADs.  This is exemplified by the CFTR promoter that in different cell types interacts with distinct sets of distal cell type-specific regulatory elements that are all located within the same TAD.  Finally, we find that long-range associations between loci located in different TADs are also detected but these display much lower interaction frequencies than looping interactions within TADs.  Interestingly, interactions between TADs are also highly cell type-specific and often involve loci clustered around TAD boundaries.  These data point to key roles of invariant TAD boundaries in constraining as well as mediating cell type-specific long-range interactions and gene regulation.

overall_design: We investigated a 2.8 Mb region on Chromosome 7 (hg18 chr7: 115797757-118405450) containing the ENCODE region ENm001 42.  The 5C experiment was designed to interrogate looping interactions between HindIII fragments containing transcription start sites (TSSs) and any other HindIII restriction fragment (distal fragments) in the target region.  Libraries were generated for five cell lines: Caco2, Calu3, Capan1, GM12878 and HepG2, with two biological replicates for each line.  5C probes were designed at HindIII restriction sites (AAGCTT) using 5C primer design tools previously developed and made publicly available online at our My5C website (http://my5C.umassmed.edu).  Probes were designed based on the ENCODE manual region 1 (ENM001) design 25 with additional probes placed throughout the region when appropriate.  We also added probes to extend the analysis to include a 700 Kb gene desert region located directly adjacent to ENM001.  Probe settings were: U-BLAST, 3; S-BLAST, 100; 15-MER, 3,000; MIN_FSIZE, 250; MAX_FSIZE, 20,000; OPT_TM, 65; OPT_PSIZE, 40.  We designed 74 reverse 5C probes, and 605 forward 5C probes.

middle: M

last: Smith

first: Gaurav

last: Jain

first: Job

last: Dekker


title: miRNA expression data from mouse fetus ear (pinnae) and back tissues

status: Public on Dec 31 2015

city: Mexico

first: Sara

last: Frias

state: Distrito Federal

address: Insurgentes Sur 3700-C 6o piso

department: Investigación en Genetica Humana/Medicina, Genómica y Toxicología Ambiental

country: Mexico

institute: Instituto Nacional de Pediatría/Instituto de Investigaciones Biomedicas, UNAM

summary: There is not information regards the role of miRNAs in the development of the external ear in mammals. The aim of this study was to determine the stage-specific expression of miRNAs during external ear development in order to identify miRNAs and their possible targets.

overall_design: GeneChip miRNA 3.0 arrays by Affymetrix were used to obtain miRNA expression profiles from mice fetal pinnae and skin back tissues at 13.5 dpc and 14.5 dpc, biological quadruplicates for each tissue were analyzed; one litter represents one biological replica, each litter with 16 fetuses in average.

first: Leda

last: Torres

first: Ulises

last: Juarez

first: Laura

last: Garcia

first: Juan

last: Miranda-Rios


title: Neuroblastoma cell line gene expression profiling

city: Duarte

first: Linda

last: Malkas

address: 1500 E. Duarte Rd

institute: City of Hope

summary: Gene expression profiles in 5 MYCN-amplified, 3 non-MYCN-amplified, and 2 non-malignant cell lines were analyzed.

overall_design: 5 MYCN-amplified, 3 non-MYCN-amplified, and 2 non-malignant cell lines were profiled without any pre-treatment.

first: Long

last: Gu

first: Robert

last: Hickey


title: Differential expression of mRNAs in porcine endometrium

city: wuhan

first: Jiangnan

last: Huang

state: Hubei

address: Shizishan Street

institute: Huazhong (Central China) Agricultural University

summary:
The study allowed for the determination of the mRNAs that were differentially expressed in porcine endometrium on different gestational day and breed. The majority of the mRNAs were differentially expressed during the implantation stage. This study will provide the information to better understanding of the role of these differently expressed mRNAs in the porcine endometrium during pregnancy.
Affymetrix mRNA arrays were used to generate mRNA profiles of on the endometrium of Meishan and Yorkshire pigs on days 15 (implantation stage), 26 (post-implantation stage) and 50 (mid-gestation stage) of gestation.

overall_design: The endometrium from different gestational day and breed were collected. In order to determine the mRNA expression profile of these tissue, RNA was extracted, labeled and hybridized on an Affymetrix mRNA array.

first: Mei

last: Yu


title: An integrative analysis of renal miRNA- and mRNA-expression signatures in progressive chronic kidney disease [discovery cohort]

city: Innsbruck

first: Michael

last: Rudnicki

address: Anichstrasse 35

department: Internal Medicine IV, Nephrology

country: Austria

institute: Medical University Innsbruck

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

summary:
MicroRNAs (miRNAs) significantly contribute to chronic kidney disease (CKD) progression via regulating mRNA expression and abundance. However, their association with clinical outcome remains poorly understood. We performed large scale miRNA and mRNA expression profiling on cryo-cut renal biopsy sections from n=43 subjects. miRNAs differentiating stable and progressive cases were determined, and putative target mRNAs showing inversely correlated expression profiles were identified and further characterized. We found a downregulation of 7 miRNAs in the progressive phenotype, and an upregulation of 29 target mRNAs which are involved in inflammatory response, cell-cell-interaction, apoptosis, and intracellular signaling. Particularly a diminished expression of miR-206 in progressive disease correlated significantly with the upregulation of the target mRNAs CCL19, CXCL1, IFNAR2, NCK2, PTK2B, PTPRC, RASGRP1, and TNFRSF25, all participating in inflammatory pathways. Progressive cases also showed a decreased expression of miR-532-3p, and an increased expression of target transcripts MAP3K14, TNFRSF10B/TRAIL-R2, TRADD, and TRAF2, all being involved in apoptosis pathways. miR-206, miR-532-3p and all 12 mRNA targets correlated with the degree of histological damage.
The identified renal miRNA- and mRNA-profiles, and biological pathways may represent regulatory mechanisms, which are commonly present in various kinds of progressive chronic kidney disease.

overall_design: mRNA- and miRNA-profiling was performed on renal biopsy samples from human subjects with various proteinuric nephropathies, miRNA-mRNA correlations were identified for those subjects who showed a progressive decline of renal function during follow up.

first: Paul

last: Perco


title: Expression data from Arabidopsis root tips rRBr mutant

status: Public on Dec 23 2015

city: Wageningen

first: Gabino

last: Sanchez-Perez

address: Droevendaalsesteeg 1

department: Bioscience

country: Netherlands

institute: Wageningen University

summary:
The RETINOBLASTOMA–RELATED (RBR) is a key regulator of cell proliferation and differentiation in plants, and plays an important role in maintenance of the stem cell niche in the root.
We used microarray analysis to characterize the transcriptional response of Arabidopsis thaliana root tips from rRBr mutant (7 samples) against Col-0 wild type (6 samples) after 4, 6 and 10 das.

overall_design: Using the Affymetrix ATH1 GeneChips, we followed the transcriptional dynamics underlying the phenotypic changes due to RBR silencing we have analysed the rRbr line at early time points of development (4, 6 and 10 das) and compared to Col-0 wild-type. Biological replicates were performed for each sample and hybridized to the chips.

first: Beatrix

last: Horvath

first: Hana

last: Kourova

first: Szilvia

last: Nagy

first: Edit

last: Nemeth

first: Zoltan

last: Magyar

first: Csaba

last: Papdi

first: Zaki

last: Ahmad

first: Serena

last: Perilli

first: Ikram

last: Blilou

first: Aladár

last: Pettkó-Szandtner

first: Zsuzsanna

last: Darula

first: Tamas

last: Meszaros

first: Pavla

last: Binarova

first: Laszlo

last: Bogre

first: Ben

last: Scheres


title: Examination of SUUR and Pc chromatin proteins in slivary glands in presence or absence of SuUR mutation using DamID technique

status: Public on Jan 10 2016

city: Novosibirsk

first: Daniil

last: Maksimov

address: Lavrentjeva ave., 8/2

country: Russia

institute: MCB NSC RAS

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Heterochromatin contains repressively modified histones and replicates late in S phase of the cell cycle. Besides the shortage in replication origins, little is known about replication timing regulation in silenced regions. In Drosophila polytene cells, late replication results in under-replication and decreased DNA copy number in heterochromatic regions of the genome. The Suppressor of Under-replication (SUUR) protein controls this feature – in its absence the DNA polytenization level in most silenced regions is restored, however the repressive histone marks are lost. We hypothesized that SUUR regulates the re-establishment of repressive histone pattern during replication which results in delayed replication completion of heterochromatin. Measuring DNA copy number in mutants with disrupted repressive pathways, we found that under-replication is directly linked to repressive histone marks supply. DamID-seq and ChIP-seq experiments revealed that SuUR mutation does not affect the establishment of heterochromatin domains. Here, we identified a novel SUUR protein interaction (CG12018) that supports SUUR association with replication complex. SUUR loads onto replication forks shortly after the origin firing and participates in chromatin maintenance rather than its establishment. Thus, our findings provide comprehensive evidence that late replication in Drosophila is caused by the time-consuming process of replication-coupled repressive chromatin renewal.

first: Olga

middle: V

last: Posukh

first: Stepan

middle: N

last: Belyakin

middle: A

first: Dmitry

middle: E

last: Koryakov

first: Ksenia

last: Skvortsova

first: Galina

last: Pokholkova


title: Maize (Zea mays) leaf transcriptome analysis under abiotic stress in wild type and RNA Polymerase IV mutant

status: Public on Jan 14 2016

city: Bologna

first: Cristian

last: Forestan

state: BO

address: Viale Fanin 44

department: Dipartimento di Scienze e Tecnologie Agro-alimentari (DISTAL)

country: Italy

institute: University of Bologna

summary: Plants have developed complex mechanisms to respond and adapt to abiotic stresses, coupling elaborate modulation of gene expression together with the preservation of genome stability. Epigenetic mechanisms - DNA methylation, chromatin modifications and non coding RNAs - were shown to play a fundamental role in stress-induced gene regulation and may also result in genome destabilization, with the activation and/or the transcription of silenced transposons and retroelements, causing genome rearrangements and novel gene expression patterns.  Maize leaf transcriptome was analyzed by total RNA-Seq in both B73 and rmr6 (PolIV mutant involved in siRNA biogenesis and in the RdDM pathway) after drought and salt stress application. Reference annotation based transcript assembly allowed the identification both of new expressed loci and splicing variants, improving the current maize transcriptome annotation. Many antisense transcripts matching on the opposite strand of annotated loci were also identified, while more than the 20% of transcripts represent non coding RNA belonging to four classes: siRNAs, shRNAs, lncRNAs and transposable elements (or their relics). Several lncRNAs are modulated by stress application while TE-related sequences are mainly expressed in rmr6 and up-regulated by the stress.

overall_design: Total RNA-Seq analysis of maize leaves from wt and rmr6-1 mutant plants grown under 1) control conditions, 2) drought stress, 3) salt stress,  4) salt+drought stress. Each condition was investigated in triplicate after 10 days of treatment and after 7 days of recovery. Samples derived from replicates 2 and 3 were pooled and sequenced together

first: Riccardo

last: Aiese-Cigliano

first: Silvia

last: Farinati

first: Alice

last: Lunardon

last: Varotto


title: Transcriptomic analysis of human B cell responses to vaccination

city: Atlanta

first: Ali

middle: Hassan

last: Ellebedy

state: GA

address: 1462 Clifton Rd NE

institute: Emory University

summary:
Analysis of the gene expression profiles of naïve B cells, resting memory B cells (MBCs), activated B cells (ABCs) and antibody-secreting cells (ASCs) isolated from peripheral blood one week following influenza vaccination.
Upon antigen exposure B cells eventually bifurcate into two distinct lineages, plasmablasts and memory B cells. We previously reported that plasmablasts or antibody-secreting cells (ASCs) could be transiently detected in blood shortly after infection or vaccination of humans. Here, we define the phenotype and the transcriptional program of a novel human antigen-specific B cell subset, referred to as activated B cells (ABCs). ABCs do not spontaneously secrete antibodies and possess a unique transcriptional profile that distinguishes them from ASCs and resting memory B cells. Clonal lineages present among day 7 ABCs persisted in blood for up to three months post-influenza immunization indicating that ABCs may be destined to join the long-term memory B cell pool. ABCs and ASCs can be clearly distinguished in blood following influenza and Ebola virus infections. Interrogating ABCs will expand our understanding of the differentiation, maturation and longevity of human B cell responses.

overall_design: Total RNA was isolated from 10,000 cells of each population.

first: Rafi

last: Ahmed


title: Expression data from MCF-7 and MCF-7/ADR cells

status: Public on Jan 05 2016

first: Cun

last: Wang

address: No. 25/Ln 2200 Xie-Tu Road, Shanghai 200032, China

institute: Shanghai Cancer Institute

summary:
Chemoresistance in breast cancer has been a great interest in past studies, however, the development of rational therapeutic strategies targeting chemoresistant cells is still a challenge for clinical oncology.The resistant property of MCF7/ADR cells was confirmed by long term culture with Dox, cell viability, and PARP cleavage assays.
Microarray analysis was performed to compare the global differences of gene expression between MCF-7 and MCF-7/ADR cells.

overall_design: MCF-7 and MCF-7/ADR gene expression profiles were analyzed. Total RNA were prepared for analysis with Affymetrix Human U133 Plus 2.0 arrays according to the manufacturer’s instructions.

first: Haojie

last: Jin


title: A new Agilent 15K cross strain P. falciparum microarray optimized for the transcriptome analysis of Indian P. falciparum isolates

status: Public on Jan 17 2016

city: Pilani

first: Ashis

middle: Kumar

last: Das

state: Rajasthan

address: Vidya Vihar

department: Biological Sciences

country: India

institute: Birla Institute of Technology & Science,Pilani (Pilani Campus)

summary: Genomic variation is an inherent phenomena observed among members of same species belonging to different geographical locations.  In case of P. falciparum, an apicomplexan protozoan parasite, its 22.8 MB nuclear genome is known to display vast genetic diversity in the subtelomeric compartments having but not exclusively variant gene families like var, rifins and stevors and examples in other elements of the genome have recently been documented. Microarrays, relies solely on the genomic sequence information to capture the relevant transcript abundance and needs to consider these variations into account for revealing true transcriptional variation.Here, we describe the designing strategy of a custom P. falciparum 15K array using Agilent platform to study the transcriptome of Indian field isolates for which genome sequence information is limited. Array contains probes representing genome sequence of two distinct geographical isolates (i.e 3D7 and HB3) and subtelomeric var gene sequence of a third isolate (IT4) known to adhere in culture condition. Probes in the array have been selected based on their efficiency to detect transcripts by performing a 244K array experiment representing multiple probes per gene/transcript. Array performance was evaluated and validated using RNA materials from P. falciparum clinical isolates obtained directly from patients with differing clinical conditions due to malaria infection.Due to pre probe screening large percentage (91 %) of the represented transcripts could be detected from Indian P. falciparum isolates. Replicated probes and multiple probes representing the same gene showed perfect correlation between them suggesting good probe performance. Additional transcripts could be detected due to inclusion of unique probes representing HB3 strain transcripts. Variant surface antigen (VSA) transcripts were detected by optimized probes representing the VSA genes of three geographically distinct strains.

overall_design: Plasmodium falciparum isolates were collected from patients (n=13) with differing clinical conditions. The patients exhibited symptoms categorized as uncomplicated (n=6) or complicated malaria (n=7). Criteria for determination of complicated disease were based on World Health Organization year 2000 guidelines. Microarray array based transcriptional profiling was carried out to evaluate the performance of the array.

first: Amit

middle: K

last: Subudhi

first: P

last: Boopathi

first: Dhanpat

last: Kochar

first: Sanjay


title: Brain microvessels ontogeny-ERI-INSERM28

city: Rouen

first: Philippe

last: Leroux

address: Boulevard Gambetta, 22

institute: INSERM-Rouen University

summary: Enriched forebrain microvessels from P5, P10 and adult mice. Transcript comparisons identified 5873 genes with FC>2 between ages and 93 pathways. The observations were confronted to proteome study using NanoLS-MS/MS and deposited on proteomeXchange platform under # PXD001718. The 2 techniques converge towards extracellular matrix, cell adhesion and junction pathways, indicating early changes in development.  The difference are examined as putative structural basis of very preterm intracerbral hemorrhage,

overall_design: 3 age comparisons of 5 days, 10 days and adult brain microvessels, 2 replicates, Agilent Whole Mouse Genome Oligo 4×44K Microarray

first: Baptiste

last: Porte

first: Bruno

last: Gonzalez

first: Michele

last: Hauchecorne

first: Jean

last: Flaman

first: Yasmine

last: Zerdoumi

first: Thierry

last: Lequerré

first: Céline

last: Derambure

first: Stéphane

last: Marret


title: GWAS for drug response in patients with OCD

status: Public on Jan 08 2016

city: Tokushima

first: Hidehiro

last: Umehara

address: 3-18-15 Kuramoto-cho

country: Japan

institute: Tokushima University Graduate School

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

summary: The goal of the present study was to identify genetic variants that are associated with drug response of OCD patients.

overall_design: We performed a genome-wide association study of 96 OCD patients to examine genetic variants contributing to the drug response of OCD patients.

first: Shusuke

last: Numata

first: Atsushi

last: Tajima

first: Akira

last: Nishi

first: Masahito

last: Nakataki

first: Issei

last: Imoto

first: Satsuki

last: Sumitani

first: Tetsuro

last: Ohmori


title: Transcriptome profiling of post-mature green seeds from Arabidopsis ddcc mutant and wild-type

status: Public on Jan 01 2016

city: Los Angeles

first: Bob

last: Goldberg

address: 610 Charles E Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

summary: The role of on-CG methylation in seed development and dormancy remains unknown. There are four genes in charge of non-CG methylation in Arabidopsis: drm1, drm2, cmt2 and cmt3. The majority of non-CG methylation in vegetative tissues, leaf, is gone in homozygous ddcc mutant line (Hume et al., 2014). To uncover the possible role of non-CG DNA methylation in seed development and dormancy, we characterized the transcriptome of ddcc mutant in Arabidopsis post-mature green seeds using Illumina sequencing. Meanwhile, post-mature green seeds from wild type were used as control.

overall_design: Illumina sequencing of transcripts from post-mature green seeds of ddcc mutant and wild type. Two biological replicates were collected.

first: Robert

first: Jer-Young

last: Lin

first: Min

last: Chen


title: Expression data of differentiated adipocyte treated with small molecules

status: Public on Jan 09 2016

city: Suwon

first: Seo-Hyuk

last: Chang

address: 2066, Seobu-ro, Jangan-gu

country: South Korea

institute: Sungkyunkwan University

summary:
To treat obesity and its related metabolism, small molecules can be used. To investigate the role of small molecules, butein, sulfuretin, and resveratrol were treated in differentiated adipocytes to find important regulators in adipocyte biology.
Each small molecules have their own charactaristics on adipocyte biology, comparison of expression profiles among three small molecules can offer new insight in adipocyte biology.

overall_design: Fully differentiated C3H10T1/2 adipocytes were treated with butein, sulfuretin, and resveratrol for 6 hours and the expression profiles were compared to find common anti- or pro-adipogenic factors.

first: No-joon

last: Song

first: Kyewon

last: Park


title: Identification of HOXB8 and K LK11 expression levels as potential biomarkers to predict the effects of FOLFOX4 chemotherapy

city: Fuzhou

first: Xingrong

last: Lu

address: No. 29, Xinquan Road, Gulou District

institute: Affiliated Union Hospital of Fujian Medical University

summary:
To measure global gene expression in primary advanced colorectal cancer patients who have undergone fluorouracil, leucovorin and oxaliplatin (FOLFOX4)  chemotherapy and screen valuable biomarkers to predict the effects of chemotherapy
Samples from primary advanced colorectal cancer patients were collected. The effects of chemotherapy were evaluated, and patients were divided into an experimental group and a control group.

overall_design:
All patients underwent standard FOLFOX4 regimen chemotherapy in four cycles after signing the chemotherapy agreement; subsequently, they were evaluated in accordance with the Response Evaluation Criteria In Solid Tumors (RECIST).Each samplewas collected immediately following resection. Each sample was divided in half: one half was fixed in formalin and embedded in paraffin; the other half floated in ice-cold phosphate-buffered saline and was stored in liquid nitrogen until total RNA extraction.
CEL files available for only 16/30 samples. Remaining CEL files have been lost.


title: Expression response of human monocyte derived macrophages to dexamethasone over a 24h time series

status: Public on Dec 17 2015

city: Easter Bush

first: Alasdair

middle: W

last: Jubb

state: Midlothian

address: The Roslin Institute

department: Roslin Institute

country: United Kingdom

institute: University of Edinburgh

summary: Macrophages are amongst the major targets of glucocorticoids (GC) as therapeutic anti-inflammatory agents.  Here we show that GC treatment of mouse and human macrophages initiates a cascade of induced gene expression including many anti-inflammatory genes. Inducible binding of the glucocorticoid receptor (GR) was detected at candidate enhancers in the vicinity of induced genes in both species and this was strongly associated with canonical GR binding motifs.  However, the sets of inducible genes, the candidate enhancers, and the GR motifs within them, were highly-divergent  between the two species.. The data cast further doubt upon the predictive value of mouse models of inflammatory disease.

overall_design: Four biological replicates of a 6 point 24h time series transcriptional response of human monocyte derived macrophages to dexamethasone 100nM.

first: Wendy

last: Bickmore

first: David

last: Hume

middle: S

last: Young


title: Enhanced engraftment, proliferation, and therapeutic potential in heart using optimized iPSC-derived cardiomyocytes

city: Kyoto

first: Yoshinori

last: Yoshida

address: 53, Kawahara-cho, Shogoin, Sakyo-ku

institute: Kyoto University

summary: Human pluripotent stem cell-derived cardiomyocytes (CMs) are a promising tool for cardiac cell therapy. To optimize graft cells for cardiac reconstruction, we compared the engraftment efficiency of intramyocardially-injected undifferentiated-induced pluripotent stem cells (iPSCs), day4 mesodermal cells, and day8, day20, and day30 purified iPSC-CMs after initial differentiation by tracing the engraftment ratio (ER) using in vivo bioluminescence imaging. This analysis revealed the ER of day20 CMs was significantly higher compared to other cells. Transplantation of day20 CMs into the infarcted hearts of immunodeficient mice showed significant functional improvement. Moreover, the imaging signal and ratio of Ki67-positive CMs at 3 months post injection indicated engrafted CMs proliferated in the host heart. Although this graft growth reached a plateau at 3 months, histological analysis confirmed progressive maturation from 3 to 6 months. These results suggested that day20 CMs had very high engraftment, proliferation, and therapeutic potential in host mouse hearts.

overall_design: Differentiated cells, N=10  Undifferentiated pluripotent stem cells, N=1  Heart samples, N=6

first: S

last: Funakoshi

first: Y

first: M

last: Narita


title: Divergent transcriptional activation by glucocorticoids in mouse and human macrophages is the result of gain and loss of enhancers

summary:
Macrophages are amongst the major targets of glucocorticoids (GC) as therapeutic anti-inflammatory agents.  Here we show that GC treatment of mouse and human macrophages initiates a cascade of induced gene expression including many anti-inflammatory genes. Inducible binding of the glucocorticoid receptor (GR) was detected at candidate enhancers in the vicinity of induced genes in both species and this was strongly associated with canonical GR binding motifs.  However, the sets of inducible genes, the candidate enhancers, and the GR motifs within them, were highly-divergent between the two species.

This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Transcriptional response of yeast cells upon high-level expression of modified GFPs

city: Japan

first: Hisao

last: Moriya

state: Okayama

address: 3-1-1 Tsushima-Naka

department: RCIS

institute: Okayama University

summary: Transcriptome yeast cells expressing modified GFPs were analyzed to elucidate the consequences of growth defect

overall_design: 7 samples were analyzed. In each sample, differently modified GFP is highly expressed. One of them is a empty vector control.

first: Koji

last: Makanae


title: An integrative analysis of renal miRNA- and mRNA-expression signatures in progressive chronic kidney disease [validation cohort]

first: Michael

last: Rudnicki

summary: MicroRNAs (miRNAs) contribute to chronic kidney disease progression via negatively regulating mRNA abundance. However, their association with clinical outcome remains poorly understood. We performed large-scale miRNA and mRNA expression profiling on cryo-cut renal biopsy sections from a discovery (n=43) and a validation (n=29) cohort. In the discovery cohort (GEO Series accession number GSE45980), miRNAs differentiating stable and progressive cases were determined, and putative target mRNAs showing inversely correlated expression profiles were identified. We found a downregulation of 7 miRNAs in the progressive phenotype, and an upregulation of 29 target mRNAs that are involved in inflammatory response, cell-cell-interaction, apoptosis, and intracellular signaling. Reduced expression of miR-206 in progressive disease correlated with the upregulation of the target mRNAs CCL19, CXCL1, IFNAR2, NCK2, PTK2B, PTPRC, RASGRP1, and TNFRSF25, all participating in inflammatory pathways. Progressive cases also showed a lower expression of miR-532-3p and an increased expression of cognate target transcripts MAP3K14, TNFRSF10B/TRAIL-R2, TRADD, and TRAF2, all being involved in apoptosis pathways. In the independent validation cohort (this set of arrays), we confirmed the decreased expression of miR-206 and miR-532-3p, and the inverse correlation of these miRNAs with the expression of 9 of the 12 target genes. The levels of the identified miRNAs and the target mRNAs correlated to histological damage indices. These results suggest the involvement of specific miRNAs and mRNAs in biological pathways associated with the progression of chronic kidney disease.

overall_design: mRNA- and miRNA-profiling was performed in a discovery cohort (n=43) and in a validation cohort (n=29) of renal biopsy samples from human subjects with various proteinuric nephropathies. In the discovery cohort, miRNA-mRNA correlations were identified for those subjects who showed a progressive decline of renal function during follow up. These profiles were reproduced in the validation cohort.

first: Paul

last: Perco


title: The transcriptome and methylome of neonatal murine hearts

status: Public on Dec 30 2015

city: Gdansk

first: Pawel

last: Sachadyn

address: Narutowicza 11/12

department: Molecular Biotechnology and Microbiology

country: Poland

institute: Gdansk University of Technology

type: Methylation profiling by genome tiling array

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


title: Comparative expression analysis of BRCA1mosMe fibroblast vs. BRCA1wt fibroblasts

city: Mainz

first: Anna

last: Etzold

state: Germany (Deutschland)

address: Langenbeckstr. 1

institute: Universität Mainz

summary: We performed a comprehensive molecular and cellular analysis of primary dermal fibroblasts taken from a patient with recurrent cancers, harboring a BRCA1 mosaic epimutation  (BRCA1mosMe) in comparison to their isogenic control fibroblasts (BRCA1wt), taken from the patient´s healthy monozygous sister.

overall_design: 4 independent samples per individual

first: Ulrich

last: Zechner


title: Comparative analysis of genome-wide gene expression profiles in hearts of C57B/6J mice

summary: The neonatal murine heart is able to regenerate after severe injury, however this capacity quickly diminishes within the first week of life. Since DNA methylation is one of epigenetic mechanisms that plays a crucial role in cell development and gene expression regulation, we explored the changes of DNA methylation and gene expression patterns which accompany the loss of the transient regenerative potential in the heart. We used MeDIP-chip approach in order to compare global DNA methylation profiles in the murine hearts at 1 day and 7 days after birth, as well as, in hearts of mice at the age of 2 and 8 weeks. The comparison exposed a number of DNA promoter regions significantly changing their DNA methylation status between these time-points. As the result a number of DMRs have been identified which show an overrepresentation of genes which are critical for proper heart maturation and muscle development. The methylome transition from d1 to d7 is characterized by the excess of gene regulatory regions which gain over those that lose DNA methylation, thus suggesting that a number of genes active at d1 are repressed at d7.

overall_design: 8 samples, each sample is a pool representing three animals

first: Paweł


title: Expression data from a 24h time series of dexamethasone treatment for mouse bone marrow derived macrophages

summary: Macrophages are amongst the major targets of glucocorticoids (GC) as therapeutic anti-inflammatory agents.  Here we show that GC treatment of mouse and human macrophages initiates a cascade of induced gene expression including many anti-inflammatory genes. Inducible binding of the glucocorticoid receptor (GR) was detected at candidate enhancers in the vicinity of induced genes in both species and this was strongly associated with canonical GR binding motifs.  However, the sets of inducible genes, the candidate enhancers, and the GR motifs within them, were highly-divergent between the two species.

overall_design: 3 biological replicates of a 6 point time series for the transcriptional response to dexamethasone 100nM

first: Robert


title: Gene expression analysis of KLF4 expression in THP-1 cells with CRISPR knockout of miR-150 and p21 (CDKN1A)

city: Seattle

first: Vivian

middle: G.

last: Oehler

state: Washington

address: 1100 Fairview Ave N. D5-100

department: Clinical Research Division

institute: Fred Hutchinson Cancer Research Center

summary: Analysis of gene expression changes associated with KLF4 expression in the AML cell lines THP1 cells. Resutls demonstrate KLF4 promotes myeloid differentiation in these cells via gene signatures. We also identified KLF4 downstream regulators that are modified in miR-150 and p21 (CDKN1A) CRISPR knockdown cells.

overall_design: Total RNA isolated from THP1 cells infected with KLF4 or empty control (ECV) lentivirus 5 days post infection (dpi), CRISPR cells were 17 days post selection.

middle: G


title: An integrative analysis of renal miRNA- and mRNA-expression signatures in progressive chronic kidney disease

city: Innsbruck

address: Anichstrasse 35

institute: Medical University Innsbruck


title: Gene expression profilings of normal human oral keratinocyte (HOK) and dysplastic oral keratinocyte cell line from a heavy smoker (DOK)

city: Zhunan Miaoli County

first: Chia

middle: Huei

last: Lee

address: 35, Keyan Rd.

department: National Institute of Cancer Research

country: Taiwan

institute: Taiwan National Health Research Institute

summary: In our previous study, we identified global genetic and epigenetic aberrations in the tumors of oral squamous cell carcinoma (OSCC) patients who were habitual smokers. We hypothesized that cigarette smoke might play a role in oral malignant transformation. DOK cell line is a dysplasitc oral keratinocyte derived from a heavy smoker with OSCC. The differentially expressed genes between DOK and normal human oral keratinocytes (HOK) may provide important information about OSCC carcinogenesis mediated by cigarette smoking.

overall_design: Total RNA was collected from DOK and HOK cells followed by gene expression microarray analysis.

first: Chia-Huei

first: Pin-Pin

last: Lin


title: Global analysis of genes regulated by canonical Wnt pathway

status: Public on Dec 25 2015

first: Hidekazu

last: Tsukamoto

address: 1333 San Pablo Street MMR414

department: Pathology

institute: University of Southern California

summary:
Up-regulation of canonical Wnt signaling has been implicated in liver fibrosis and cancer.
To determine canonical Wnt target genes potentially implicated in these diseases, we performed microarray analysis of culture-activated rat hepatic stellate cells (HSCs) treated with canonical Wnt inhibitors, DKK-1, ICG-001, or FJ9.

overall_design: DKK-1, ICG-001, and FJ9 treatment of HSCs: Fully activated primary rat HSCs (cultured for 7 days on plastic dish with 10% FBS containing low glucose DMEM) were treated with: 1) adenovirus expressing DKK-1 (Ad.DKK-1) vs. Ad.GFP (control) at a multiplicity of infection (MOI) of 200 for 24 h in low glucose DMEM with 5% FBS and antibiotics, and then maintained for an additional 24 h in serum-free medium; 2) ICG-001 (10 µM) vs. vehicle for 24 h in serum-free medium; or 3) FJ9 (200 µM) vs. vehicle for 24 h in serum-free medium. No replicates were used. Instead, each of the 6 conditions (3 treatments and 3 respective controls)/samples consisted of a pool of RNA from 3 to 4 rats.

first: Keane

last: Lai


title: RNA Seq analysis of sorted Schmidtea mediterranea X1 and Xins cells to identify factors specific to neoblasts

city: Happy Valley

first: Alex

middle: Daniel

last: Chitsazan

state: OR

address: 2720 S Moody Ave

institute: Oregon Health and Science University

summary: Adult stem cells are tissue-specific cells with the capacity to self-renew and differentiate to continually replace cells lost to normal physiological turnover or injury. Neoblasts, the planarian stem cells, are widely distributed throughout the body mesenchyme, driving constitutive renewal of tissues during homeostasis and endowing planarians with the remarkable capacity to regenerate wholly from tiny tissue fragments. Neoblasts are the only dividing cells in planarians and are believed to be collectively comprised of both a heterogeneous population of pluripotent cells with broad differentiation potential and also lineage-committed progenitor cells that give rise to specific tissues. Recent technology has allowed one to isolate stem cells so we used a well-established method to isolate planarian stem cells by Hoechst blue staining and flow cytometry. To understand the molecular mechanisms underlying neoblast differentiation, we performed an RNA-Seq analysis of X1 and Xins cells looking at the differentially expressed genes between the two populations.

overall_design: Examine gene expression profiles of adult flatworm’s X1 and Xins cell types. The experiment was performed in quadruplicate yielding a total of 8 samples.

first: Elizabeth

last: Duncan

middle: D

first: Chris

last: Seidel

first: Alejandro

last: Sanchez Alvarado


title: Set1 and MLL1/2 target distinct sets of functionally different genomic loci in vivo


title: Tissue expression profiling of miRNAs in Amur sturgeon (Acipenser schrenckii)

city: Guangzhou

first: zhang

middle: xiu

last: juan

state: Guangdong province

address: NO.105, Xingang west road, Haizhu district

institute: Guangdong Entomological institute

summary: Microarray expriments were performed in 5 tissues of Amur sturgeon, included liver, spleen, brain ,muscle and heart.

overall_design: We designed total 615 mature miRNAs probes  and 5 probes repulication in microarray experiments.

first: Xiujuan

last: Zhang

first: Jinpin

last: Chen


title: Methyl-CpG-binding domain (MBD) sequencing of 15 primary stage 4S neuroblastoma tumors

status: Public on Dec 15 2015

city: Ghent

first: Anneleen

last: Decock

address: De Pintelaan 185

country: Belgium

institute: Ghent University

type: Methylation profiling by high throughput sequencing

summary: The DNA methylome of 15 primary stage 4S neuroblastoma tumors is profiled by enrichment with a methyl-CpG-binding domain (MBD) and massively parallel sequencing

overall_design: DNA of 15 primary stage 4S tumors is sheared (fragments of ± 200 bp), followed by MBD-based (MethylCap kit of Diagenode) enrichement, library preparation and multiplexing. Both input DNA and captured DNA were sequenced paired-end on Illumina Hiseq2000

first: Maté

last: Ongenaert

first: Frank

last: Speleman

first: Jo

last: Vandesompele


title: NPM‐ALK permits the survival of thymic T cells with aberrant T cell receptor rearrangements enabling thymic escape and tumor development

city: Marseille

first: Mohamed

last: BELHOCINE

address: 163, Avenue de Luminy

institute: INSERM

type: Genome variation profiling by genome tiling array

summary: We present evidence to support a new model of Anaplastic Large Cell Lymphoma (ALCL) pathogenesis in which the malignancy is initiated in early thymocytes, prior to TCR rearrangement which is bypassed in NPM‐ALK transgenic mice following Notch1 expression. In support, we show that T cell receptor (TCR) rearrangements are aberrant in some human ALCL, yielding events that would not normally be permissive for survival during T cell development. However, a TCR is required for thymic egress and subsequent development of peripheral tumors in mice yet this TCR must be down‐regulated for T‐cell lymphomagenesis. Children affected by ALCL may thus harbor lymphoma-initiating cells in the thymocyte population that seeds relapse after chemotherapy.

overall_design: comparative genomic hybridization data from 43 human Anaplastic Large Cell Lymphoma (ALCL) samples and control samples

first: Tim

last: Malcolm

first: Patrick

last: Villarese

first: Camilla

last: Fairbairn

first: Laurence

last: Lamant

first: Amélie

last: Trinquand

last: Hook

first: Amos

last: Burke

last: Brugières

first: Katherine

last: Hughes

first: Dominique

last: Payet

first: Olaf

last: Merke

first: Ana‐Iris

last: Schiefer

first: Shahid

last: Mian

first: Mariusz

last: Wasik

first: Martin

last: Turner

first: Lukas

last: Kenner

first: Vahid

last: Asnafi

last: Macintyre

first: Suzanne


title: Effect of DBC1/CCAR2 knockout on global gene expression in SW480 cells

city: Seoul

first: Jeong

middle: Hoon

last: Kim

address: Irwon-dong Gangnam-gu

summary:
Deleted in breast cancer (DBC1; also known as CCAR2) is a coactivator for nuclear receptors (NRs) and other transcription factors as well as a negative regulator of epigenetic modifiers such as deacetylases SIRT1 and HDAC3.
We performed genome-wide gene expression analysis in wild-type and DBC1 knockout SW480 cells to investigate global gene expression changes induced by DBC1 knockout.

overall_design: Total RNAs were isolated from SW480 wild-type and DBC1 knockout cells using the RNeasy mini kit (Qiagen). The integrity of RNA was analyzed using an Agilent 2100 Bioanalyzer. Three independent biological replicates were assayed for each sample. The microarrays were performed following the Affymetrix standard protocol.

first: Eun

middle: J

last: Yu

middle: H


title: Endurance training in early life results in long-term programming of heart mass in rats

status: Public on Dec 09 2015

city: Burwood

first: Glenn

middle: David

last: Wadley

state: Victoria

address: 221 Burwood Highway

country: Australia

institute: Deakin University

summary:
This study aimed to examine if early life exercise could normalize the reduced heart mass we have previously observed in the adult hearts from growth restricted rats.
We investigated the molecular pathways using microarray analysis to explain how endurance exercise in early life might be regulating the sustained increase in heart mass we have observed in these rats in adulthood. At 5 weeks of age, male WKY rats were allocated to one of the following exercise treatments: remained sedentary with post mortem (PM) at 9 or 24 weeks, early exercise training (from 5-9 weeks of age) with PM at 9 or 24 weeks, or later exercise training (from 20-24 weeks of age) with PM at 24 weeks (n=8 males/group). Exercise training involved treadmill running 5 days/ week for 4 weeks. Running duration progressively increased from 20 up to 60 minutes per day, with the treadmill speed set at 15 m/min for the first week and 20 m/min thereafter. At 9 or 24 weeks of age rats were killed with an intraperitoneal injection of Ilium Xylazil-20 (30 mg/kg) and Ketamine (225 mg/kg). The rats in the 9 week old early exercise and 24 week old later exercise groups were killed 72 hours following the last bout of treadmill running. Total RNA was obtained from the whole-hearts for analysis

overall_design: Total RNA obtained from the hearts of WKY rats. Male offspring remained sedentary or underwent treadmill running from 5-9 weeks (early exercise) or 20-24 weeks of age (later exercise).


title: PARP-1 regulation of alternative splicing

status: Public on Dec 01 2015

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

summary: To address the global impact of PARP-1 on alternative splicing, we isolated total RNA in two biological replicates from control (non-treated), PARP-1 siRNA- and PJ-34-treated cells. Sequencing of these RNAs on an Illumina HiSeq 2500, yielded >56 million 100-bp paired-end RNA-seq reads. First we tested if PARP-1 KD was effective at the RNA-seq level. Read aligning to the entire gene body of PARP-1 shown a reduction in PARP-1 expression of about 1.5-fold (P-value < 0.0003), confirming that indeed PARP-1 was depleted after PARP-1 siRNA treatment. We next used these RNA-seq data sets (control, PARP-1 KD and PARylation inhibited) to assess whether these treatments resulted in changes in i) gene expression and ii) alternative splicing.

overall_design: mRNA profiles of two biological replicates (non-treated), two PARP-1 siRNA knockdowns (100ng and 500ng) and two PARylation inhibition PJ-34-treated cells (10uM and 0.3uM) were compared using RNA-Seq on an Illumina HiSeq 2500.

first: Elena

last: Matveeva

first: John

last: Maiorano

first: Qingyang

last: Zhang

first: Abdallah

middle: M

last: Eteleeb

first: Paolo

last: Convertini

middle: C

first: Stefan

last: Stamm

first: Jiping

last: Wang

first: Yvonne

last: Fondufe-Mittendorf


title: Prp4 Kinase Grants the License to Splice:  Control of Weak Splice Sites during Spliceosome Activation

city: Barcelona

first: Jose

last: Ayte

address: Doctor Aiguader 88

country: Spain

institute: Universitat Pompeu Fabra

summary: The genome of the fission yeast Schizosaccharomyces pombe encodes 17 kinases that are essential for cell growth. These include the cell-cycle regulator Cdc2, as well as several kinases that coordinate cell growth, polarity, and morphogenesis during the cell cycle. In this study, we further characterized another of these essential kinases, Prp4, and showed that the splicing of many introns is dependent on Prp4 kinase activity. For detailed characterization, we chose the genes res1 and ppk8, each of which contains one intron of typical size and position. Splicing of the res1 intron was dependent on Prp4 kinase activity, whereas splicing of the ppk8 intron was not. Extensive mutational analyses of the 5’ splice site of both genes revealed that proper transient interaction with the 5’ end of snRNA U1 governs the dependence of splicing on Prp4 kinase activity. Proper transient interaction between the branch sequence and snRNA U2 was also important. Therefore, the Prp4 kinase is required for recognition and efficient splicing of introns displaying weak exon1/5’ splice sites and weak branch sequences.

overall_design: RNAseq was performed on three samples in which a conditional mutant was analyzed in three time point (time 0, 30 and 60 minutes).

first: Luca

last: Cozzuto


title: New global miRSeq analysis of “miRNome”: the example of PTC and nodal metastases

city: Brussels

first: Manuel

last: Saiselet

address: 808 route de Lennik

institute: ULB - IRIBHM

type: Non-coding RNA profiling by high throughput sequencing

summary: The set of expressed microRNAs in a given cell type, or “miRNome”, can be explored under many different aspects. Many studies report modulations of the miRNome in a wide variety of cancers. Papillary thyroid cancer is the most prevalent type of endocrine cancer. The presence of nodal metastases increases the risk of recurrence and mortality. In our study, we performed microRNA deep sequencing (miRSeq) of 3 PTC, their matching normal tissues and nodal metastases and designed a new bioinformatic framework to analyze variations of the different aspects of the miRNome: expression profile, isomiRs and non-templated additions distributions, mutation or A-to-I RNA-editing. Furthermore, we validated our results using qRT-PCR on independent samples from 14 patients and using the collection of miRSeq data from The Cancer Genome Atlas (up to 495 miRseq of PTC). We gave a particular attention to cell content and contamination. We showed that microRNA expression profiles of thyrocytes are altered during tumorigenesis. These alterations involve known up regulations of microRNAs such as miR-146b-5p or miR-22-3p but also down regulations such as miR-7-5p, miR-7-2-5p, miR-1179 or miR-204-5p. Furthermore, some expression modulations were increased following the nodal metastatic process such as miR-7-2-3p or miR-138-1-3p. However, we did not find variations in the other aspects of the miRNome analyzed. We used our bioinformatic frameworks on the largest PTC miRSeq data collection available, to our knowledge. It allowed us, in one study on the different aspects of the miRNome, to find modulated microRNAs that could act as biomarkers of PTC.

overall_design: We performed microRNA deep sequencing (miRSeq) of 3 PTC, their matching normal tissues and nodal metastases and designed a new bioinformatic framework to analyze variations of the different aspects of the miRNome: expression profile, isomiRs and non-templated additions distributions, mutation or A-to-I RNA-editing.

first: David

last: Gacquer

first: Myriam

last: Decaussin-Petrucci

first: Alex

last: Spinette

first: Ligia

last: Craciun

first: Guy

last: Andry

first: Vincent

last: Detours

first: Carine

last: Maenhaut


title: Expression data on F0 and F1 strains of Pseudomonas aeruginosa

status: Public on Dec 04 2015

city: Singapore

first: Wee Siang

last: Lim

address: 20 Biopolis Way, Centros

country: Singapore

institute: A*STAR BTI

summary: In our study, we seek to understand the differences in growth physiology between wild type P. aeruginosa PAO1 (F0 strain) and its PB1-phage resistant derivative (F1 strain).

overall_design: F0 and F1 cells were harvested at mid-log for RNA extraction for hybridization to Affymetrix GeneChip P. aeruginosa genome array. A total of 4 biological replicates (4 F0 and 4 F1 samples were used).

first: Wee


title: Genome wide binding of glucocorticoid receptor in dexamethasone treated human monocyte derived macrophages

city: Easter Bush

first: Alasdair

last: Jubb

address: The Roslin Institute

institute: University of Edinburgh

summary: Macrophages are amongst the major targets of glucocorticoids (GC) as therapeutic anti-inflammatory agents.  Here we show that GC treatment of mouse and human macrophages initiates a cascade of induced gene expression including many anti-inflammatory genes. Inducible binding of the glucocorticoid receptor (GR) was detected at candidate enhancers in the vicinity of induced genes in both species and this was strongly associated with canonical GR binding motifs.  However, the sets of inducible genes, the candidate enhancers, and the GR motifs within them, were highly-divergent  between the two species.. The data cast further doubt upon the predictive value of mouse models of inflammatory disease.

overall_design: human monocyte derived macrophages were treated with dexamethasone for 2h, fixed and ChIP performed. Material from 4 volunteers was pooled for the IP.

first: Wendy

middle: A

last: Bickmore

last: Hume

first: Robert

last: Young


title: Role of Estrogen Receptor α in Mouse Oviduct Gene Expression

status: Public on Dec 08 2015

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: Estrogen receptor α (ERα) is a nuclear transcription factor crucial for the female reproductive function. We previously reported that mice lacking epithelial ERα in the epithelial cells of female reproductive tract (Wnt7aCre+;Esr1fl/fl, conditional knockout or cKO) were infertile, in part, due to an implantation defect. To determine if oviductal dysfunction also contributed to their infertility, we examined the fertilization rates and embryo development in vivo during the first few days of pregnancy. At 0.5 days post coitum (dpc), cKO females had significantly fewer zygotes than wild type control littermates (WT). At 1.5 dpc, cKO females had no 2-cell embryos at all; only dead oocytes or embryos and empty zona pellucidas were observed. These results indicate that lack of ERα in the oviductal epithelium resulted in alterations in the oviductal microenvironment that were detrimental to the embryos. Microarray analysis revealed dramatic differences in gene expression between cKO and WT oviducts collected at 0.5 dpc and significant but less dramatic differences at 1.5 dpc. These findings indicate that signaling via epithelial ERα is essential to generate an oviductal milieu supportive of fertilization and embryo development.and may have implications for infertility in women.

overall_design: The oviduct samples were collected from female reproductive tract epithelial ER α knockout (cKO) and wild type control littermates (WT) at days 1 and 2 of pregnancy (0.5 and 1.5 days post coitum). Each experimental group contains 4 replicates. Gene expression analysis was conducted by using Agilent Whole Mouse Genome 4×44 multiplex format oligo arrays (no. 014868; Agilent Technologies, Santa Clara, CA)

first: Wipawee

last: Winuthayanon

first: Sylvia

last: Hewitt

first: Elizabeth

last: Padilla-Banks

first: Grant

last: Orvis

first: Richard

middle: R

last: Behringer

first: Carmen

last: Williams

first: Kenneth

last: Korach


title: The effect of palmitate on gene expression profile in proliferating myoblasts

status: Public on Nov 25 2015

city: Warsaw

first: Zofia

last: Wicik

state: mazovia

address: Pawinskiego 5

department: Department of Human Epigenetics

institute: Mossakowski Medical Research Center

summary:
High-fat diet or exposure to saturated fatty acids affects skeletal muscle growth and function. The aim of the present study was to investigate the effect of palmitate on the transcriptomic profile of mouse C2C12 myoblasts. Global gene expression was evaluated using whole mouse genome oligonucleotide microarrays, and the results were validated through real-time PCR. A total of 4047genes were identified as differentially expressed, including 3492 down-regulated and 555 up-regulated genes during 48-h-exposure to palmitate (0.1 mmol/l). Functional classification showed the involvement of PA-regulated genes in several processes which regulate cell growth. In conclusion, palmitate modifies the expression of genes associated with: i) myoblast responsiveness to hormones and growth factors, ii) cytokine and growth factor expression, and iii) regulation of cell-cell cell-matrix communication. Such alterations can affect myoblast growth and differentiation, however further studies in this field are required.
To whom the correspondence should be addressed: Dr K. Grzelkowska-Kowalczyk; e-mail: k_grzel_kow@poczta.fm, tel/fax: (48 22) 847 24 52

overall_design: After scanning of hybridized microarrays, quantitation of slide images was performed using Feature Extraction Software (Agilent) using default parameters and the raw data were exported to GeneSpring GX 12 (Agilent, Santa Clara, CA) and log2 transformed. For identification of genes significantly altered in cell compared with the control normal gene set. Total detected entities were filtered by flags (detected, non detected) and error (coefficient of variation: CV < 50.0 percent) to remove very low signal entities and to select reproducible signal values of entities among the replicated experiments, respectively. In statistical analysis, separated for experiment with myoblasts treated with  palmitate acid was used t-test unpaired (p < 0.05) with multiple testing correction: Benjamini-Hochberg <0.05, all significant changes over fold change 1.6 were selected.

first: Kamil

last: Grabiec

first: Alicja

last: Majewska

first: M

last: Milewska

last: Błaszczyk

first: Katarzyna

last: Grzelkowska-Kowalczyk


title: Genome wide binding of glucocorticoid receptor in dexamethasone treated mouse bone marrow derived macrophages

middle: W

last: Jubb

summary: Macrophages are amongst the major targets of glucocorticoids (GC) as therapeutic anti-inflammatory agents.  Here we show that GC treatment of mouse and human macrophages initiates a cascade of induced gene expression including many anti-inflammatory genes. Inducible binding of the glucocorticoid receptor (GR) was detected at candidate enhancers in the vicinity of induced genes in both species and this was strongly associated with canonical GR binding motifs.  However, the sets of inducible genes, the candidate enhancers, and the GR motifs within them, were highly-divergent between the two species.

overall_design: Mouse bone marrow derived macrophages were generated from two male 10 week old C57BL/6 mice, treated with dexamethsone 100nM or vehicle and glucocorticoid receptor bound DNA extracted by chromatin immunoprecipitation

last: Bickmore

first: David


title: Genome-wide maps of PARP-1-bound nucleosomes.

status: Public on Nov 30 2015

city: Grand Rapids

first: Yvonne

middle: Nsokika

last: Fondufe-Mittendorf

state: MI

address: 333 Bostwick Ave NE

department: Epigenetics

institute: Van Andel Institute

summary: PARP-1 binds to specific nucleosomes to regulate gene activity. While PARP-1's role in transcription inititaion is known, a surprising finding here was that PARP-1 is highly enriched at exon-intron and intron-exon boundaries, sort of demarcting exons. This indicating a role in alternative splicing.

overall_design: ChIP-seq of PARP1-bound nucleosomes as well as MNase-seq of total nucleosome in Drosophila S2 cells

first: Elena

last: Matveeva

first: John

last: Maiorano

first: Qingyang

last: Zhang

first: Eteleeb

last: Abdallah

first: Paolo

last: Convertini

first: Eric

last: Rouchka

first: Stefan

last: Stamm

first: Jiping

last: Wang

last: Fondufe-Mitteendorf


title: Gene expression analysis of CMV infected human fibroblasts in two cultures with differing sensitivity to the virus

city: Moscow

first: Alina

last: Artcibasova

address: Samory Mashela, 1

institute: Federal Research Center of Pediatric Hematology, Oncology and Immunology

summary: Analysis of gene expression patterns in cytomegalovirus infected human fibroblasts for two cultures with differing sensitivity to the virus

overall_design: Total RNA obtained from 2 human fibroblast lines with differing sensitivity to CMV infection. For each line 3 types of samples are compared: pre-experimantal norm, 3 hours after infection, 3 hours without infection.

middle: V

first: Anastasia

last: Zabolotneva

first: Maria

last: Suntsova

first: Anton

last: Buzdin


title: IBMCP JLeon lab NO-exposed (15, 30 and 60 min after pulse of 300 ppm NO during 5 min) wt Col-0 versus untreated wt Col -0

city: Valencia

first: Jose

last: Leon

address: CPI Edificio 8E, Ingeniero Fausto Elio s/n

institute: IBMCP (CSIC-UPV)

summary:
Compared analysis of the transcriptomes of 12-day old seedlings from wild type  Col-0 treated with NO for 15, 30 and 60 min vs untreated control seedlings.
Samples were harvested 12 h after dawn of day 12 after sowing and seedlings were grown under long days (16 h light / 8 h darkness) photoperiodic conditions.

overall_design: 12 distributed as 3 independent biological replicates of untreated, NO-treated 15 min, NO-treated 30 min and NO-treated 60 min.

first: José

last: León


title: A robust single primate neuroepithelial cell clonal expansion system for neural tube development and disease studies

status: Public on Nov 21 2015

city: Kunming

first: Tianqing

last: Li

address: No. Boda Road, Yuhua Area, Chenggong New Town

country: China

institute: Primate Translational Medicine Research Center, Kunming University of Science and Technology

summary: Developing a model of primate neural tube (NT) development is important to promote many NT disorder studies in model organisms. Here, we report a robust and stable system to allow for clonal expansion of single monkey neuroepithelial stem cells (NESCs) to develop into miniature NT-like structures. Single NESCs can produce functional neurons in vitro, survive and extensively regenerate neuron axons in monkey brain. NT formation and NESC maintenance depend on high metabolism activity and Wnt signaling. NESCs are regionally restricted into a telencephalic fate. Moreover, single NESCs can turn into radial glial progenitors (RGPCs). The transition is accurately regulated by Wnt signaling through regulation of Notch signaling and adhesion molecules. Finally, using the “NESC-TO-NTs” system, we model the functions of folic acid (FA) on NT closure and demonstrate FA can regulate multiple mechanisms to prevent NT defects. Together, our system is ideal for studying NT development and diseases.

overall_design: compare gene expression profiles in  monkey neuroepithelial stem cells (NESCs), newly converted radial glial progenitor cells (RPGCs) from NESCs and  differentiated neurons from NESCs

first: Xiaoqing

last: Zhu

first: Bo

first: Zongyong

last: Ai

first: Zheng

last: Xiang

first: Kunshang

first: Xiaoyan

last: Qiu

first: Yongchang

last: Chen

first: Yuemin

first: Joshua

last: Rizak

first: Yuyu

last: Niu

first: Xintian

last: Hu

first: Yi

last: Sun

first: Weizhi

last: Ji


title: Single-cell transcriptional profiling of Th17 cells, differentiated in vitro for 48h [IL1B_IL6_IL23-48h-IL-17A/GFP+]

status: Public on Nov 20 2015

city: Berkeley

first: Nir

last: Yosef

state: CA

address: Berkeley

department: EECS

country: USA

institute: UC Berkeley

summary: Extensive cellular heterogeneity exists within specific immune-cell subtypes classified as a single lineage, but its molecular underpinnings are rarely characterized at a genomic scale. Here, we use single-cell RNA-seq to investigate the molecular mechanisms governing heterogeneity and pathogenicity of Th17 cells isolated from the central nervous system (CNS) and lymph nodes (LN) at the peak of autoimmune encephalomyelitis (EAE) or polarized in vitro under either pathogenic or non-pathogenic differentiation conditions. Computational analysis reveals a spectrum of cellular states in vivo, including a self-renewal state, Th1-like effector/memory states and a dysfunctional/senescent state. Relating these states to in vitro differentiated Th17 cells, unveils genes governing pathogenicity and disease susceptibility. Using knockout mice, we validate four novel genes: Gpr65, Plzp, Toso and Cd5l (in a companion paper). Cellular heterogeneity thus informs Th17 function in autoimmunity, and can identify targets for selective suppression of pathogenic Th17 cells while sparing non-pathogenic tissue-protective ones.

first: Jellert

last: Gaublomme

first: Aviv

last: Regev


title: Single-cell transcriptional profiling of Th17 cells, differentiated in vitro for 48h [TGFB1_IL6-48h]


title: Single-cell transcriptional profiling of Th17 cells, differentiated in vitro for 48h [TGFB1_IL6-48h-IL-17A/GFP+]


title: Single-cell transcriptional profiling of Th17 cells, harvested at peak of disease in EAE from LN [EAE-LN-IL-17A/GFP+]


title: microRNA expression analysis of CMV infected human fibroblasts in two cultures

first: Alina

last: Artcibasova

summary: Analysis of microRNA expression patterns in cytomegalovirus infected human fibroblasts for two cultures with differing sensitivity to the virus

overall_design: Non-coding RNAs were cloned from total RNA extracts obtained from 2 human fibroblast lines with differing sensitivity to CMV infection. For each line 3 types of samples are compared: pre-experimantal norm, 3 hours after infection, 3 hours without infection.

first: Anastasia

last: Zabolotneva

first: Olga

last: Kovalchuk

first: Anton

last: Buzdin


title: Population transcriptional profiling of Th17 cells, isolated from CNS or LN at peak of disease in EAE


title: Single-cell transcriptional profiling of Th17 cells, harvested at peak of disease in EAE from CNS [EAE-CNS-IL-17A/GFP+]


title: Population transcriptional profiling of Th17 cells, isolated from the lamina propria of the large intestine from 3-6 month old IL-17GFP KI mice


title: Genomic analysis of xCT-mediated regulatory network: identification of novel targets against AIDS-associated lymphoma

status: Public on Nov 23 2015

city: New Orleans

first: Zhiqiang

last: Qin

state: LA

address: 1700 Tulane Ave

institute: LSUHSC-NO

summary: Kaposi’s sarcoma-associated herpesvirus (KSHV) is the etiological agent of primary effusion lymphoma (PEL), a rapidly progressing malignancy mostly arising in HIV-infected patients. Even under conventional chemotherapy, PEL continues to portend nearly 100% mortality within several months, which urgently requires novel therapeutic strategies. We have previously demonstrated that targeting xCT, an amino acid transporter for cystine/glutamate exchange, induces significant PEL cell apoptosis through regulation of multiple host and viral factors. More importantly, one of xCT selective inhibitors, Sulfasalazine (SASP), effectively prevents PEL tumor progression in an immune-deficient xenograft model. In the current study, we use Illumina microarray to explore the genomic gene profile altered by SASP treatment within 3 KSHV+ PEL cell-lines, and discover that many genes involved in oxidative stress/antioxidant defense system, apoptosis/anti-apoptosis/cell death, and cellular response to unfolded proteins/topologically incorrect proteins are potentially regulated by xCT. We further functionally validate 2 downstream candidates, OSGIN1 (Oxidative stress-induced growth inhibitor 1) and XRCC5 (X-ray repair cross-complementing protein 5), their relationship with PEL cell survival/proliferation and chemoresistance, respectively. Together, our data indicate that targeting these xCT-regulated novel downstream genes may help devise promising therapeutic strategies against PEL and/or other AIDS-related lymphoma.

overall_design: 3 KSHV PEL cell lines were treated with xCT selective inhibitor Sulfasalazine (SASP) and the gene expression signature was compared to that of untreated cells

first: Lu

last: Dai

first: Yueyu

last: Cao

first: Yihan

first: Johnan

last: Kaleeba

first: Jovanny

last: Zabaleta


title: Population transcriptional profiling of KO or WT cells,, differentiated in vitro for 48-96h towards Th17 cells


title: Methyl-CpG-binding domain (MBD) sequencing of 42 primary neuroblastoma tumors

status: Public on Nov 19 2015

city: Ghent

first: Anneleen

last: Decock

address: De Pintelaan 185

summary: The DNA methylome of 42 primary neuroblastoma tumors is profiled by enrichment with a methyl-CpG-binding domain (MBD) and massively parallel sequencing

overall_design: DNA of 42 primary tumors is sheared (fragments of ± 200 bp), followed by MBD-based (MethylCap kit of Diagenode) enrichement, library preparation and multiplexing. Captured DNA fractions were sequenced paired-end on Illumina Genome Analyzer IIx.

first: Maté

last: Ongenaert

first: Frank

last: Speleman

first: Jo

last: Vandesompele


first: Nir

overall_design: Population transcriptional profiling of in vitro polarized Th17 cells, either sorted for IL17A/GFP+ or unsorted.


title: Methyl-CpG-binding domain (MBD) sequencing of 45 primary neuroblastoma tumors

summary: The DNA methylome of 45 primary neuroblastoma tumors is profiled by enrichment with a methyl-CpG-binding domain (MBD) and massively parallel sequencing

overall_design: DNA of 45 primary tumors is sheared (fragments of ± 200 bp), followed by MBD-based (MethylCap kit of Diagenode) enrichement, library preparation and multiplexing. Both input DNA and captured DNA were sequenced paired-end on Illumina Hiseq2000


title: GPCR expression in mouse dorsal root ganglia (DRG)

city: Frankfurt am Main

first: Klaus

last: Scholich

state: Hessen

address: Theodor Stern Kai 7

department: Clinical Pharmacology

country: Germany

institute: Hospital of Goethe University

summary: RNA of dorsal root ganglia from untreated adult mice (6-8 weeks) was tested for GPCR expression

overall_design:
quantitative RT-PCR was performed and the copy number was normalized to the amount of cDNA (ng)
Institute of Clinical Pharmacology, pharmazentrum frankfurt/ZAFES, Hospital of the Goethe-University Frankfurt, Germany
Max Planck Institute for Heart and Lung Research, Department of Pharmacology, 61231 Bad Nauheim, Germany


title: Murine iTreg cells: Control (MIEG3) vs. YY1-expression vector transduced

status: Public on Nov 17 2015

city: Seoul

first: Gap Ryol

last: Lee

address: 35 Baekbeom-ro, Mapo-gu

department: Department of Life Science

institute: Sogang University

summary: Transcriptional profiling of mouse induced Treg (iTreg) cells comparing control (MIEG3) vector-transduced iTreg cells with iTreg cells transduced with YY1-overexpression vector. Tranduced cells were sorted by GFP expression. Goal was to determine the effects of YY1 on global iTreg gene expression.

overall_design: Two-condition experiment, iTreg(control MIEG3) vs. iTreg(YY1-overexpressing). Biological replicates: 1 MIEG3 vs. YY1.

first: Gap


title: Methyl-CpG-binding domain (MBD) sequencing of neuroblastoma tumors

institute: Ghent University

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

overall_design: Refer to individual Series


title: CMV infected human fibroblasts in two cultures with differing sensitivity to the virus

first: Alina


title: Optimizing sgRNA structure to improve CRISPR-Cas9 knockout efficiency

city: El Paso

first: Ying

last: Dang

state: TX

address: 5001 El Paso Dr

institute: TTUHSC

summary: The current commonly used single-guide RNA (sgRNA) structure has a shortened duplex compared with the native bacterial clustered regularly interspaced short palindromic repeats RNA (crRNA)–transactivating crRNA (tracrRNA) duplex. Here we show that modifying the sgRNA structure by extending the duplex length and mutating the fourth T of the continuous sequence of Ts (which is the pause signal for RNA polymerase III [pol III]) to C or G significantly, and sometimes dramatically, improves knockout efficiency in cells. In addition, the new sgRNA structure also significantly increases the efficiency of more challenging genome-editing procedures, such as gene deletion, which is important for inducing a loss-of-function in non-coding genes.

overall_design: Gene editing efficiency of different sgRNA design in TZM-bl cells

first: Haoquan

last: Wu


title: Screen mRNAs specifically regulated by mTORC1 in calvarial osteoblasts from mice

status: Public on Nov 07 2015

city: Guangzhou

first: Bin

last: Huang

address: No.1838 North Guangzhou Avenue

institute: Southern Medical University

summary: To screen mRNAs specifically regulated by mTORC1, a global mRNA expression profile in calvarial osteoblasts (OBs) from mice with or without OB-specific Tsc1 knockout was developed using microarray.

overall_design: Wild type (WT) or OB-specific Tsc1 knockout (KO) mice were sacrificed, with calvarial osteoblasts harvested and subjected to total RNA extraction.

first: Xiaochun

last: Bai


title: microRNA screening in human pancreatic adenocarcinoma

status: Public on Nov 03 2015

city: Muenster

first: Sameer

last: Dhayat

address: Albert-Schweitzer-Campus 1 ( W1)

institute: Comprehensive Cancer Center Muenster


title: MicroRNA screening in human pancreatic carcinoma cell lines

summary:
No reliable predictors of susceptibility to gemcitabine chemotherapy exist in pancreatic ductal adenocarcinoma. MicroRNAs (miR) are epigenetic gene regulators with tumorsuppressive or oncogenic roles in various carcinomas. This study assesses chemoresistant PDAC for its specific miR expression pattern.
Gemcitabine-resistant variants of two mutant p53 human pancreatic adenocarcinoma cell lines were established. MicroRNA screening was investigated by microarray.

overall_design: Gemcitabine-resistant PANC-1 (PANC-1-GR) and MIA-PaCa-2 (MIA-PaCa-2-GR) cell clones were produced by exposing the parental cells to repeated pulsatile gemcitabine treatment over 3 days with constant sublethal concentrations followed by recovery-periods with agent-free medium until the cells recovered exponentially. Parental PANC-1 cells were treated with 0.4µM gemcitabine cycles for approximately 9 months. Parental MIA-PaCa-2 cells were exposed to 0.06µM gemcitabine cycles for approximately 12 months. Affymetrix GeneChip miRNA microarrays (Affymetrix UK Ltd., High Wycombe, UK) were performed in parental and chemoresistant PANC-1  and MIA-PaCa-2 cells after 29 chemotherapy cycles using the manufacturers´ protocols. The samples were prepared from 1µg of total-RNA in accordance with the Affymetrix FlashTag Biotin HSR RNA Labeling Kit. The targets were hybridized overnight to Affymetrix GeneChip miRNA arrays. Following hybridization, the arrays were washed and stained using the Affymetrix GeneChip Fluidics Station 450 and scanned using the Affymetrix GeneChip Scanner 3000 7G. Microarray data quality was checked as recommended by the manufacturer and by the quality metrics in the Partek Genomics Suite software (Partek Inc., St. Louis, MO).

first: Jochen

last: Seggewiß


title: miRNA profile in the vitreous of proliferative vitreoretinal disease patients

status: Public on Nov 02 2015

city: Tomioka Urayasu

first: Ayumi

last: Ouchi

state: Chiba

department: Ophthalmology

institute: Juntendo University Urayasu Hospital

type:
Expression profiling by RT-PCR
Other

summary: The microRNA profiles in the vitreous of proliferative vitreoretinal disease (PVD) such as proliferative diabetic retinopathy with fibrovascular membrane and macular hole (MH) patients were studied by RT-PCR.

overall_design: From each individual in the two cohorts: the PVD (n=3) and MH patients (n=3), vitreous specimens were collected and microRNAs were extracted for miRNA profiles analysis.


title: Next Generation Sequencing Methylation Profiling in Skeletal Muscle from Lean and Obese Subjects [Microarray expression]

status: Public on Nov 01 2015

city: Tempe

first: Samantha

middle: Elaine

last: Day

state: AZ

address: University Dr. and Mill Ave.

institute: Arizona State University

summary: Obesity is a metabolic disease caused by environmental, genetic, and epigenetic factors.  However, the epigenetic mechanisms of obesity are incompletely understood. The aim of our study was to identify skeletal muscle DNA methylation patterns in combination with transcriptomic changes in obesity.

overall_design: Muscle biopsies were obtained basally from lean (n=10) and obese (n=10) participants in combination with euglycemic hyperinsulinemic clamps to assess insulin sensitivity. We performed microarray (SurePrint G3 Human Gene Expression 8x60K v2) analysis on RNA isolated from vastus lateralis muscle biopsies. This represents the expression profiling component only.

middle: E

first: Dawn

middle: K

last: Coletta

first: Richard

middle: L


title: Next Generation Sequencing Methylation Profiling in Skeletal Muscle from Lean and Obese Subjects [Bisulfite-Seq]

summary: Obesity is a metabolic disease caused by environmental, genetic, and epigenetic factors.  However, the epigenetic mechanisms of obesity are incompletely understood. The aim of our study was to identify skeletal muscle DNA methylation patterns in obesity.

overall_design: Muscle biopsies were obtained basally from lean (n=11) and obese (n=9) participants in combination with euglycemic hyperinsulinemic clamps to assess insulin sensitivity. We performed reduced representation bisulfite sequencing next generation methylation analysis on DNA isolated from vastus lateralis muscle biopsies.


title: Next Generation Sequencing Methylation Profiling in Skeletal Muscle from Lean and Obese Subjects


title: Gene expression analysis of CALGB 9741 patient tumor samples using the nCounter RUO-PAM50 signature

status: Public on Nov 10 2015

city: Saint Louis

first: Sherri

last: Davies

state: MO

address: 4950 Parkview Place

institute: Washington University

summary: Intrinsic subtyping of breast cancer was performed using an nCounter RUO-PAM50 gene expression assay to determine the ability of instrinsic subtyping to predict what patients may benefit from altered chemotherapy  scheduling in the CALGB 9741 clinical trial population.

overall_design: FFPE primary breast tumor samples archived at the CALGB Pathology Coordinating Office (PCO) were used to obtain total RNA for instrinsic subtyping using the nCounter Analysis System. Gene-expression profiles were generated for 1321 of 1471 patient samples (90%) suitable for inclusion in this study.


title: RBFox2 regulates a broad RNA program and is required for genome-wide targeting of polycomb complex

status: Public on Oct 22 2015

city: La Jolla

first: Xiang-Dong

last: Fu

address: 9500 Gilman Drive, Room 231

department: CMM

institute: UC San Diego

summary: Increasing evidence suggests that diverse RNA binding proteins interact with regulatory RNAs to regulate transcription. RBFox2 is a ubiquitous RNA binding protein with prevalent expression in stem cells, heart, and brain. Here, we report a systematic dissection of the RBFox2-regulated RNA program in the mouse heart, demonstrating its essential function for organizing the contractile apparatus and excitation-contraction (EC) coupling by modulating alternative splicing and microRNA activity. In this analysis, we unexpectedly encounter a major functional intersection between RBFox2 and Polycomb Complex 2 (PRC2), revealing a central requirement for RBFox2 to mediate genome-wide targeting of the PRC2 complex and transcriptional repression via chromatin-associated nascent RNAs. These findings unveil the mechanism underlying the enigmatic association of PRC2 with numerous active genes, highlight the importance of gene body sequences to gauge transcriptional output, and suggest nascent RNAs as critical signals for transcriptional feedback control to maintain homeostatic gene expression in mammalian cells.

overall_design:
RASL-seq in cardiac myocytes (from WT and RBFox2 KO mouse hearts at ages of week 5, week 9 and week 18);
RBFox2 whole cell and nucleus CLIP-seq in cardiac myocytes (from WT mouse hearts at age of week 9);
Ago2 CLIP-seq in cardiac myocytes (from WT and RBFox2 KO mouse hearts at age of week 9);
3'-end RNA-seq in cardiac myocytes (from WT and RBFox2 KO mouse hearts at age of week 9);
GRO-seq in mouse hearts (from WT and RBFox2 KO mice at age of week 9) and cultured MEF cells (negative control RNA, RBFox2 siRNA or SUZ12 siRNA treatment);
RBFox2 and SUZ12 CHIP-seq in mouse hearts(from WT mice at age of week 9);
RBFox2, SUZ12 and H3K27me3 CHIP-seq in cultured MEF cells (negative control RNA, RBFox2 siRNA or SUZ12 siRNA treatment, DRB treatment).

first: Chaoliang

last: Wei

first: Yu

last: Zhou

first: Rui

last: Xiao

first: Yuanchao

last: Xue

first: Jing

last: Hu

first: Hanwei

last: Cui

first: Taiki

last: Tsutsui

first: Jinsong

last: Qiu

first: Kunfu

last: Quyang

first: Indroneal

last: Banerjee

first: Hairi

last: Li

first: Ju

last: Chen


title: Identification of novel regulators of Th17 cell pathogenicity by single-cell genomics

first: Nir

last: Yosef

first: Jellert

last: Gaublomme

first: Aviv

last: Regev


title: Chip-chip from C3H10T1/2 cells with Gli1

status: Public on Oct 15 2015

city: Shanghai

first: Lu

last: Shen

address: RM 218 Little White House 1954 Huashan RD

department: Bio-X Institutes

institute: Shanghai Jiao Tong University

type: Genome binding/occupancy profiling by genome tiling array

summary:
Indian Hedgehog signaling (IHH) regulates multiple aspects of endochondral bone formation and ultimately regulates expression of downstream genes by Gli zinc finger domain-containing transcription regulators in the cartilage development.
In response to a BDA1 mutant IHH induction, Gli1-mediated downstream regulatory pattern might be quite different from that in response to wild type IHH induction.

overall_design: Comparison of wild type IhhN protein-induced, E95K mutant IhhN protein-induced and non-protein induced cells

first: Shengying

last: Qin


title: Gene expression signatures for IhhN protein induced cells

summary: Previous studies demonstrated that hererozygous missense mutations in IHH could lead to a decreasing IHH signaling efficacy and cause brachydactyly type A1 (BDA1). For revealing difference of Gli1-mediated downstream regulatory effects between wild type IHH signaling and E95K mutant IHH signaling, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to be targets of Gli1 cis-regulation.

overall_design: Gene expressions of Wild type IhhN protein-induced or E95K mutant IhhN protein-induced  were measured after 48-hour incubation in the presence of 750nM protein. Non-protein induced cells were as control.


title: In vitro microRNA screening in human pancreatic adenocarcinoma

first: Sameer

last: Dhayat

summary:
No reliable predictors of susceptibility to gemcitabine chemotherapy exist in pancreatic ductal adenocarcinoma. MicroRNAs (miR) are epigenetic gene regulators with tumorsuppressive or oncogenic roles in various carcinomas. This study assesses chemoresistant PDAC for its specific miR expression pattern.
Gemcitabine-resistant variants of PANC-1, a mutant p53 human pancreatic adenocarcinoma cell line, were established. MicroRNA screening was investigated by microarray.

overall_design: Gemcitabine-resistant PANC-1 (PANC-1-GR) cell clones were produced by exposing the parental cells to repeated pulsatile gemcitabine treatment over 3 days with constant sublethal concentrations followed by recovery-periods with agent-free medium until the cells recovered exponentially. Parental PANC-1 cells were treated with 0.4µM gemcitabine cycles for approximately 9 months. Affymetrix GeneChip miRNA microarrays (Affymetrix UK Ltd., High Wycombe, UK) were performed in parental and chemoresistant PANC-1 cells after 17 chemotherapy cycles using the manufacturers´ protocols. The samples were prepared from 1µg of total-RNA in accordance with the Affymetrix FlashTag Biotin HSR RNA Labeling Kit. The targets were hybridized overnight to Affymetrix GeneChip miRNA arrays. Following hybridization, the arrays were washed and stained using the Affymetrix GeneChip Fluidics Station 450 and scanned using the Affymetrix GeneChip Scanner 3000 7G. Microarray data quality was checked as recommended by the manufacturer and by the quality metrics in the Partek Genomics Suite software (Partek Inc., St. Louis, MO).

first: Jochen

last: Seggewiß


title: Single-cell chromatin profiles reveal a spectrum of stem cell epigenetic states

status: Public on Oct 12 2015

city: cambridge

first: oren

last: ram

state: MASSACHUSETTS

address: 415 Main Street

department: epigenomics

institute: Broad institute

summary: Chromatin profiling provides a versatile means to chart gene regulatory elements and investigate their mechanisms of regulation. However, current methods yield ensemble profiles that are insensitive to cell-to-cell variation. This is a major limitation as transcriptional states and phenotypes vary markedly across individual cells. Here we combined microfluidics, DNA barcoding and sequencing to profile chromatin at single-cell resolution. We demonstrate the technology by profiling a mixture of ES cells, fibroblasts and hematopoietic progenitors, and deconvoluting in silico high-quality maps for each cell type. We find that regulatory elements differ in their variability, with bivalent promoters showing particularly heterogeneous patterns across single-cells that in contrast with to the relative stability of active promoters and enhancers. Finally, we document a spectrum of ES cell states whose chromatin landscapes exhibit varying degrees of pluripotency and priming signatures. Our study presents an innovative single-cell analysis tool for single-cell analysis, and reveals aspects of epigenetic heterogeneity not be captured by transcriptional analysis alone.

overall_design: Mouse embryonic Stem cells (V6.5) mouse embryonic fibroblasts (globalstem) and hematopoietic progenitor cells (EML) dissociated prior to encapsulation using trypsin and re-suspended in PBS at a concentration of about 5•106/mL. The cell suspension is loaded in a syringe together with the magnetic stirrer bar that prevents sedimentation of the cell suspension. The cell suspension is injected into a co-flow drop-maker device with a lysing buffer and MNase. We use OEM syringe pumps (KD Scientific, MA, USA) with typical flow rates of 1.8 mL/hr for the oil and 250 µL/hr for each of the aqueous phases, resulting in a drop diameter of ~50 µm. Drops are collected and incubated off chip at 4ºC for 10 minutes and 37ºC for 15 minutes to complete cell lysis and chromatin shearing.   To label cells in drops, cell-bearing drops and barcode-library drops are re-injected into a “three point merger” device. Drops are spaced on chip by oil with 0.2% w/w surfactant and are then electrocoalesced. An additional ligation buffer is pico-injected as the drops are coalesced. The device electrodes are connected to a high voltage amplifier (TREK 2210) which supplies a 100 V sine wave at a frequency of 25 kHz. The flow rates used to inject the drops are chosen to ensure that no more than one barcode drop fuses with a single cell-bearing drop, even at the expense of some drops not fusing with other drops. Typical flow rates fulfilling these requirements are 1 mL/hr for the oil, 100 µL/hr for the cell-bearing drops, 30 µL/hr for the barcode-drops and 170 µL/hr for the ligation buffer. To control the number of cells collected per sample, we measure the filling number λ at the cell encapsulation stage and use a fast camera (HiSpec1, Fastec Imaging,USA) to measure the frequency f of pairs of barcode-drops and cell-bearing drops that fuse at the labeling stage. The time T100 required to collect 100 cells is then calculated as T100= 100/λf. Typically, f=100 Hz and λ=0.1, so that 1000 pairs of fused drops are collected to sample 100 cells, and the collection lasts 10 seconds. To protect the collected drops from evaporating and adsorbing to the walls of the collection vial, they are collected into a vial containing ~50 µL of oil and 1 % w/w surfactant and 30 µL of emulsion of ~70 µm carrier drops containing only buffer. The sample is collected and incubated at room temperture for 1.5 hour to allow ligation of adapters to chromosomal DNA.   Barcodes were commercially synthesized (IDT) and delivered in three 384 well-plates at concentrations of 500 µM. To encapsulate the barcodes in drops we design 96 parallel drop-makers on a single microfluidic chip, so that the aqueous inlets of each drop-maker (22 gauge stainless steel capillaries, New England Small Tube) precisely fit one quarter of a 384 well-plate and are immersed in 96 different wells, each containing a unique barcode. Oil with 1% w/w surfactant is distributed to all drop-makers via a common inlet that is connected to a pressurized oil reservoir. The plate and the microfluidic parallel device are placed in a pressure chamber while a common outlet for all 96 barcode drop-makers is located outside the pressure chamber. Upon pressurizing the chamber, each of the 96 barcode solutions is forced through its own drop-maker, thereby forming an emulsion where every drop contains about 1 billion copies of one of the 96 barcodes. We pressurize the oil reservoir to 9 psi and the pressure chamber to 6 psi, producing ~35 µm drops at a rate of about 500 µL/min from 96 wells. After encapsulation the device is washed with water by placing it in a petri dish filled with water and pressurizing the chamber for 2 minutes. Then the device is similarly washed with isopropanol with the exception that the oil inlet is also fed with isopropanol. Finally, the device is dried by placing it in the pressurized chamber with all inlets exposed for several minutes. The process is repeated 12 times in 6 hours until a total of 1152 different barcodes are encapsulated to form the final barcode-library emulsion. A total volume of about 10 mL is produced from 10 µL in each well.

first: Assaf

last: Rotem

first: Oren

last: Ram

first: Noam

last: Shoresh