title: Gene expression profile of intestinal stem cells (ISCs) and ATOH1+ve cells in mice

city: Kamakura

first: Satoshi

last: Kondo

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: Atoh1 is the master transcription factor of intestinal secretory cells. Lineage-tracing model of Atoh1+ve cells showed that the progeny of Atoh1+ve cells can develop into either LGR5+ve or LGR5-ve cells. Present analysis compared the gene expression profile of Atoh1+ve cell-derived LGR5+ve cells and LGR5-ve cells, compared to the resident LGR5+ve cell population of the mouse small intestine.

overall_design: One-condition experiment, compared between 3 groups of cells: LGR5-ve cells of Atoh1+ve cell origin, LGR5+ve cells of Atoh1+ve cell origin and Lgr5+ve cells of other cell origin. Each cell population was collected from the mouse small intestine by fluorescence-activated cell sorting (FACS). Biological replicates: One for each sorted cell fraction. Cell sorting was performed by using pooled cells prepared from four mice. One replicate per array.

first: Fumiaki

last: Ishibashi

first: Ryuichi

last: Okamoto


title: A protein phosphatase network controls the temporal and spatial dynamics of differentiation commitment in human epidermis

status: Public on Oct 17 2017

city: London

first: ajay

last: Mishra

address: Great Maze Pond

department: Centre for Stem Cells and Regenerative Medicine

country: United Kingdom

institute: King's College London

summary: Epidermal homeostasis depends on a balance between stem cell renewal and terminal differentiation. The transition between the two cell states, termed commitment, is poorly understood. Here we characterise commitment by integrating transcriptomic and proteomic data from disaggregated primary human keratinocytes held in suspension to induce differentiation. Cell detachment induces several protein phosphatases, five of which - DUSP6, PPTC7, PTPN1, PTPN13 and PPP3CA – promote differentiation by negatively regulating ERK MAPK and positively regulating AP1 transcription factors. Conversely, DUSP10 expression antagonises commitment. The phosphatases form a dynamic network of transient positive and negative interactions that change over time, with DUSP6 predominating at commitment. Boolean network modelling identifies a mandatory switch between two stable states (stem and differentiated) via an unstable (committed) state. Phosphatase expression is also spatially regulated in vivo and in vitro. We conclude that an auto-regulatory phosphatase network maintains epidermal homeostasis by controlling the onset and duration of commitment.

overall_design: Total RNA obtained from keratinocytes which were subjected to suspension induced differentiation (time course experiment).

first: Ajay

first: Angela

middle: O

last: Pisco

first: Fiona

middle: M

last: Watt


title: mRNA sequence of Drosophila melanogaster heads to evaluate the neurological effects of larval diet on adults

status: Public on Jun 03 2017

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

country: USA

institute: NIDDK, NIH

type: Expression profiling by high throughput sequencing

summary: Drosophila melanogaster larvae reared on isocaloric diets with different protein/sugar ratios, exhibit different developmental times and the eclosed adults show different metabolite pools of glycogen and triglycerides (Matzkin et al., 2011, PMID: 21525254).  To investigate the effect of larval diet on adult neurological processes at the gene expression level we performed high throughout RNA sequencing of fly heads reared in two different protein/sugar ratio diets.

overall_design:
The design involved three factors: Diet (fixed), Sex (fixed) and Strain (random).   There were two diets.  One with a high protein/sugar ratio (HPS) and the other with a low protein/sugar ratio (LPS). We collected heads from Males (M) and Females (F) of three Drosophila melanogaster isofemales lines which were collected near University of California San Diego by T. Markow.  The three strains were collected in September of 2010 are referred to as SD2, SD3 and SD6. We performed 12 replicate (2x2x3) treatments. 70-80 heads from 2-6 h post-eclosion flies were dissected per treatment. We performed polyA selection and generated single end 75 bp reads on a total of 12 samples.

There are 13 samples in this submission because the first C1 library made failed (data not included) and when the repeat library was made (successful, data represented as GSM2187059) another library was also made for sample C7 (GSM2187065), which is labeled D1 (GSM2187066).

first: Juan

last: Hurtado

first: Mariana

last: Ramírez

first: Maria

middle: D

last: Jaime

first: Therese

last: Markow


title: Expression profile of MCF7 and T47D human breast cancer cell lines upon treatment with the BET bromodomian inhibitor JQ1

status: Public on May 08 2017

city: L'Hospitalet de Llobregat

first: Manuel

last: Castro

state: Barcelona

address: Av. Gran Vía de l'Hospitalet 199

department: PEBC

country: Spain

institute: IDIBELL

overall_design: Two breast cancer cell lines (MCF7 and T47D) were treated with 1uM JQ1 or vehicle for 24 hours. Three biological replicates were obtained for each condition.

first: M

last: Pérez-Salvia

last: Esteller


title: Gene expression profile of colonic Atoh1+ve cells and their descendants in DSS-colitis mice

status: Public on Jun 01 2017

state: Kanagawa

country: Japan

summary: Atoh1 is the master transcription factor of secretory-type intestinal epithelial cells. By using a lineage-tracing model of Atoh1+ve cells, those Atoh1+ve epithelial cells and their descendants were collected from the colon of DSS-colitis mice or from the control mice, and subjected to global gene expression analysis.

overall_design: Two-condition experiment, Atoh1+ve  epithelial cells and their descendants collected from the colon of DSS-colitis mice (DSS) vs Atoh1+ve epithelial cells and their descendants collected from the colon of untreated mice (control). Biological replicates: One for each condition, independently collected from each group of mice. One replicate per array.


title: Comparison of gene expression signatures between Cre- KTC organoid organoid and Cre+ KTC organoid

status: Public on Apr 30 2017

city: Tokyo

first: Hayato

last: Nakagawa

address: 7-3-1 Hongo Bunkyo-ku

institute: The University of Tokyo

summary: To identify downstream genes involved in cholangiocarcinoma development by genetic manipulations of Kras, TGFbR2, and CDH1, we cultured the biliary organoid from the extrahepatic bile duct of Cre-negative LSL-KrasG12D;Tgfbr2flox/flox;CDH1flox/flox (KTC) mice, and induced gene recombination using a lentivirus expressing Cre-recombinase (Cre+ KTC organoid) or control lentivirus (Cre- KTC organoid). Then, we compared gene expression signatures between Cre- KTC organoid organoid and Cre+ KTC organoid.

overall_design: Biliary organoids isolated from KTC mice were infected with Cre-expressing or control lentivirus, and transduced cells were selected using puromycin. Two weeks later, we compared gene expression signatures between Cre- KTC organoid organoid and Cre+ KTC organoid.

first: Nobumi

last: Suzuki


title: MicroRNA expression in sporadic and FAP-associated Desmoid Tumors and correlation with beta-catenin gene mutations

status: Public on May 01 2017

city: Bari

first: Maria Teresa

last: Rotelli

address: Piazza Giulio Cesare 11

department: DETO

country: Italy

institute: University of Bari

summary: Desmoid tumors (DT) are rare, benign, fibroblastic neoplasm with challenging histological diagnosis. DTs can occur sporadically or associated with the familial adenomatous polyposis coli (FAP). Most sporadic DTs are associated with β-catenin gene (CTNNB1) mutations, while mutated APC gene causes FAP disease. MicroRNAs (miRNAs) are involved in many human carcinogenesis.   The miRNA profile was analyzed by microarray in formalin-fixed, paraffin-embedded (FFEP) specimens of 12 patients (8 sporadic, 4 FAP-associated) and 4 healthy controls. One hundred and  one miRNAs were dysregulated, of which 98 miRNAs in sporadic DTs, 8 in FAP-associated DTs, 5 were shared by both tumors. Twenty-six miRNAs were then validated by RT-qPCR in 23 sporadic and 7 FAP-associated DT samples matched with healthy controls. The same qPCR method was used to evaluate the CTNNB1 mutational status in sporadic DTs. The correlation between sporadic DTs and miRNA expression showed that miR-21-3p increased in mutated versus wild-type DTs, while miR-197-3p was decreased. The mRNA expression of Tetraspanin3 and Serpin family A member 3, miR-21-3p targets, and L1 Cell Adhesion Molecule, miR-197-3p target, was also evaluated. CTNNB1 mutations associated to miRNA dysregulation could help histological diagnosis of sporadic DTs and could affect the genesis and the progression of this disease.

overall_design: To define a specific DT miRNA profile, miRNA microarray analysis on FFEP tissue samples of 8 sporadic DTs, 4 FAP-associated DTs, regardless to tumor site, and 4 control samples has been performed. After evaluation of the CTNNB1 mutational status in 23 sporadic DTs, the altered miRNA expression pattern has been correlated with mutated (M) and wild-type (Wt) sporadic DTs.

first: Aldo

last: Cavallini

first: Catia

last: Lippolis

first: Domenico

last: Piscitelli

first: Matteo

last: Accetturo

first: Rosa

last: Digennaro

first: Claudia

last: Covelli

first: Nicola

last: Carella

first: Donato

middle: F

last: Altomare


title: Intestinal MSI-1 CLIP-CHIP used for pool 2 gene prioritization

status: Public on Apr 24 2017

city: New York

first: Sagar

last: Chhangawala

state: NY

address: 1300 York Ave.

department: PBSB

institute: Weill Cornell Medical College

summary: UV-crosslinked mouse intestine was immunoprecipitated for MSI1. Similar CLIP protocol was performed in Park et al. 2015 Journal of Experimental Medicine except RNA was random primed and hybridized to Affymetrix arrays 1.0ST array. Fold enrichment was ranked over IgG.

overall_design: UV-crosslinked mouse intestine was immunoprecipitated for MSI1. Similar CLIP protocol was performed as in Park et al. 2015 Journal of Experimental Medicine except RNA was random primed and hybridized to Affymetrix arrays 1.0ST array. Fold enrichment was ranked over IgG.

first: Micheal

last: Kharas


title: RNA binding protein SYNCRIP regulates the leukemia stem cell program [RNA-Seq]

summary: RNA binding proteins (RBPs) tightly control mRNA abundance, stability and translation while mutations or altered expression of specific factors can drive malignancy1,2. However, the identity of the RBPs that govern cancer stem cell self-renewal remains poorly characterized. The MSI2 RBP is a central regulator of translation of the cancer stem cell program3-5,6. Here we report, through proteomics analysis of the MSI2 interacting RBP network and functional shRNA screening, 24 genes required for in vivo leukemia, 20 of which are direct MSI2 protein interactors. Seven of these shRNA screen hits were retested in vitro and found to be required for myeloid colony formation. SYNCRIP (also known as HNRP-Q or NSAP1) was the most differentially required gene between normal (c-kit enriched cells) and myeloid leukemia cells. SYNCRIP is highly expressed in mouse and human leukemia cells and its depletion increases apoptosis, differentiation and delays leukemogenesis. Gene expression profiling of SYNCRIP depleted cells demonstrates a loss of the MLL-AF9 and HOXA9 leukemia stem cell gene associated program. SYNCRIP interacts with MSI2 indirectly through shared mRNA targets (such as Hoxa9, Myc and Ikzf2) and MSI2 or HOXA9 overexpression rescues the effects of SYNCRIP depletion. Strikingly, the shRNA-SYNCRIP gene expression signature can predict survival in AML patients. Overall, we uncovered a functionally dysregulated riboproteome in cancer that can be further distinguished from normal cells and propose that targeting this network could result in a novel therapeutic strategy in eradicating cancer stem cells.

overall_design: Total RNA was isolated from 9 individually transduced and processed MLL-AF9 murine leukemia cells (n=3 for each group including shRNA against luciferase, two shRNAs against SYNCRIP) using TRIzol and the Qiagen RNeasy Plus® mini kit (QIAGEN, Germany).  RNA was denatured and 1st chain of cDNA was synthesized using oligo-dT primer containing illumina-compatible linker sequence. After removal of RNA 2nd cDNA chain was synthesized with random decamer containing another illumina-compatible linker sequence. Illumina compatible annealing sequences and external barcodes were introduced during amplification of the libraries.

first: Michael


title: MR-dependent transcriptional regulation of IWAT, BAT, Muscle, and Liver Gene Expression

status: Public on May 02 2017

city: Baton Rouge

first: Thomas

middle: W

last: Gettys

state: LA

address: 6400 Perkins Road

department: Nutrient Sensing and Adipocyte Signaling

institute: Pennington Biomedical Research Center

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse embryonic stem cells, neural progenitor cells and embryonic fibroblasts. We find that lysine 4 and lysine 27 trimethylation effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect cell state and lineage potential. Lysine 36 trimethylation marks primary coding and non-coding transcripts, facilitating gene annotation. Trimethylation of lysine 9 and lysine 20 is detected at satellite, telomeric and active long-terminal repeats, and can spread into proximal unique sequences. Lysine 4 and lysine 9 trimethylation marks imprinting control regions. Finally, we show that chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations and transcription effects of dietary methionine restriction in peripheral tissues.

overall_design: Examination of transcriptional effects of Control and Methionine-restricted diets across 4 tissues

first: Laura

middle: A

last: Forney

first: Desiree

last: Wanders

first: Kirsten

middle: P

last: Stone

first: Sujoy

last: Ghosh


title: Next Generation Sequencing Facilitates The Study of the Effect of ABX464 in Intestinal Inflammation

status: Public on Apr 27 2017

city: Montpellier

first: Laurent

last: MANCHON

address: 1919 Route de Mende

country: France

institute: CNRS

summary:
Purpose: The goals of this study are to establish the protective effect of ABX464 in DSS-induced colitis comparing transcript levels between cells (BMDMs) ABX464-treated stimulated or not by LPS.
Methods: 24 intestinal macrophages mRNA profiles of three distinct group of BMDM cultures from mice were generated by deep sequencing, using Illumina protocol. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: HISAT and Bowtie2 followed by genes expression quantification using a software package called RSEM.
Results: Using an optimized data analysis workflow, we mapped about 45 million sequence reads per sample to the mouse genome (build mm9) and identified 1383 expressed genes in the LPS-stimulated BMDMs among which 439 and 397 genes increased and decreased in expression >= 1.5 log2-fold, respectively. Altered expression of some genes was confirmed with qPCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to inflammatory function. Data analysis with HISAT/Bowtie2 and RSEM workflows revealed a significant overlap yet provided complementary insights in transcriptome profiling.
Conclusions: Our study represents the detailed analysis of BMDMs transcriptomes, with biologic samples, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: 24 intestinal mRNA profiles of three distinct group of BMDM cultures from mice were generated by deep sequencing, in simplicate, using Illumina platform.

first: Karim

last: Chebli

last: Papon

last: Hahne

last: Manchon

first: Jamal

last: Tazi


title: Comparison of scAAV9-CßA and scAAV9-U6 driven artificial miRNAs targeting human huntingtin

city: Worcester

first: Edith

last: Pfister

state: MASSACHUSETTS

address: 368 Plantation St, ASC4-2007

department: Medicine

institute: UMass Medical School

type: Non-coding RNA profiling by high throughput sequencing

summary: Huntington’s disease is a devastating, incurable neurodegenerative disease affecting up to 12 per 100,000 patients worldwide. The disease is caused by a mutation in the Huntingtin (Htt) gene. There is interest in reducing mutant Huntingtin by targeting it at the mRNA level but the maximum tolerable dose and long-term effects of such a treatment are unknown. Using a self-complementary AAV9 vector, we delivered a mir-155 based artificial miRNA under the control of the chicken ß-actin or human U6 promoter. In mouse brain, the artificial miRNA reduced the human huntingtin mRNA by 50%. The U6, but not the CßA promoter, produced the artificial miRNA at supraphysiologic levels.  Embedding the antisense strand in a U6-mir-30 scaffold reduced expression of the antisense strand but increased the sense strand. In mice treated with scAAV9-U6-mir-155-HTT or scAAV9-CßA-mir-155-HTT, activated microglia were present around the injection site one-month post-injection. Six-months post-injection, mice treated with scAAV9-CßA-mir-155-HTT were indistinguishable from controls. Those that received scAAV9-U6-mir-155-HTT showed behavioural abnormalities and striatal damage. In conclusion, miRNA backbone and promoter can be used together to modulate expression levels and strand selection of artificial miRNAs and in brain the CßA promoter can provide an effective and safe dose of a human huntingtin. We also performed RNAseq on total RNA. In the mice injected with AAV9-U6-anti-HTT-6433, 44 transcripts were significantly downregulated while 30 were significantly upregulated when compared to the naïve control. In the AAV-CßA-anti-HTT-6433 group, 12 transcripts were downregulated and 4 were upregulated. Overall, transcripts containing a seed sequence target are downregulated in the scAAV-U6-anti-HTT-6433 group but not the scAAV9-CßA-anti-HTT-6433 group.

overall_design: Transgenic mice expressing human huntingtin with a stretch of approximately 128 polyglutamine encoding repeats (Yac128 mice) at a vector dose of 3.0x10^9 vg/striatum with self-complementary AAV9 vectors harboring the artificial miRNA under the control of either the U6 or CBA promoter. Unless otherwise noted, there were n=3 mice/group.

middle: L

first: Christian

last: Mueller

first: Neil

last: Aronin

first: Faith

last: Conroy

first: Huaming

last: Sun


title: RNA binding protein SYNCRIP regulates the leukemia stem cell program

last: Chhangawala

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

overall_design: Refer to individual Series


title: Characterization of chordoma cell lines derived from the clivus region

status: Public on Apr 18 2017

city: Ulm

first: Kevin

last: Mellert

address: Albert-Einstein-Allee 23

department: Institute of Pathology

country: Germany

institute: University Hospital Ulm

summary: mRNA profiling of three clival chordoma cell lines. The expression profiles were compared to previously published expression profiles of sacral chodomas (GEO accession number: GSE68497) to determine whether there are differences in expression that indicate stricing differences on molecular grounds.

first: Daniela

last: Jäger

last: Barth


title: Safety and Efficacy of the JAK Inhibitor Tofacitinib Citrate for Alopecia Areata and Variants

status: Public on Apr 21 2017

city: Stanford

first: Anthony

last: Oro

state: CA

address: 269 Campus Drive, CCSR 2145c

department: Dermatology

institute: Stanford University

summary: The samples include RNA from scalp biopsies before treatment and at 8 weeks of treatment with Tofacitinib Citrate 5 mg BID in patients with Alopecia Areata. 32% had a SALT score of 50% or higher and 47% had clinically significant response.

overall_design: Open label trial of patients with Alopecia Areata of more than 6 months in duration refractory to standard therapy. Each patient took tofacitinib citrate 5mg BID for 3 months and then stopped. Biopsies were taken pretreatment and then at 8 weeks from the scalp and submitted for RNA sequencing.

first: Gautam

last: Shankar


title: Peripheral blood transcriptional analysis of a severe Ebola virus disease patient reveals dramatic transitions during critical illness and recovery

status: Public on Apr 12 2017

city: Seattle

first: kathie

last: walters

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

summary: Pearson analysis of daily gene expression signatures revealed dramatic gene expression changes in peripheral blood leukocytes (PBL) that correlated with changes in serum and PBL viral load, coagulopathy, multiple organ dysfunction and then recovery.

overall_design: Here, daily global host gene expression responses were measured in peripheral blood from a 34–year-old male health care worker exposed to EBOV in Sierra Leone and evacuated to NIH on day 7 (d7) of clinical illness through onset of critical illness and during recovery

first: Kathie-Anne

last: Walters

first: John

middle: C

last: Kash

first: Jeffery

middle: K

last: Taubenberger


title: Malaria Host Pathogen Interaction Center Experiment 04: Host and parasite gene transcript abundances, from bone marrow aspirate, of Macaca mulatta infected Plasmodium cynomolgi treated with artemether over 7 time points in a 100 day study

city: Atlanta

first: Mary

last: Galinski

state: GA

address: 954 Gatewood Road

department: Vaccine Center at Yerkes

institute: Emory University

summary: This project is part of the Malaria Host-Pathogen Interaction Center (MaHPIC) - a transdisciplinary malaria systems biology research program initially supported by an NIH/NIAID contract (# HHSN272201200031C, 2012-2017; see http://www.systemsbiology.emory.edu). The MaHPIC continues with ongoing support from the Defense Advanced Research Project Agency (DARPA) and others. The MaHPIC generates many data types (e.g., clinical, hematological, parasitological, metabolomics, functional genomics, lipidomics, proteomics, immune response, telemetry) and mathematical models, to iteratively test and develop hypotheses related to the complex host-parasite dynamics in the course of malaria in non-human primates (NHPs), and metabolomics data via collaborations with investigators conducting clinical studies in malaria endemic countries, with the overarching goal of better understanding human disease, pathogenesis, and immunity. Curation and maintenance of all data and metadata are the responsibility of the MaHPIC:  Mary Galinski mary.galinski@emory.edu (MaHPIC Program Director), Jessica Kissinger jkissinger@uga.edu (MaHPIC Co-Program Director), and Alberto Moreno alberto.moreno@emory.edu (MaHPIC Co-Program Director).

sample_organism:
Macaca mulatta
Plasmodium cynomolgi strain B

overall_design: Malaria-naive male rhesus macaques (Macaca mulatta), approximately three years of age, were inoculated intravenously with salivary gland sporozoites isolated at the Centers for Disease Control and Prevention from multiple Anopheles species (An. dirus, An. gambiae, and An. stephensi) and then profiled for parasitological, clinical, immunological, functional genomic, lipidomic, proteomic, and metabolomic measurements. The experiment was designed for 100 days, and pre- and post-100 day periods to prepare subjects and administer curative treatments respectively. The anti-malarial drug artemether was subcuratively administered to three subjects during the primary parasitemia to suppress clinical complications and to all animals for curative treatment of blood-stage infections to allow detection of relapses. One subject was euthanized during the 100-day experimental period due to clinical complications of malaria. The anti-malarial drugs chloroquine and primaquine were administered to all remaining subjects at the end of the study for curative treatment of the liver- and blood-stage infections, respectively. Plasma samples were acquired every other day from capillary blood and at seven-time points from venous blood.  The seven-time point collections were used to generate these results.  This dataset was generated from bone marrow aspirate samples from 5 individuals collected 7 times over the 100-day experiment. Since one animal was euthanized after time point 3, a total of 31 samples were collected.  The experimental design and protocols for this study were approved by the Emory University Institutional Animal Care and Use Committee (IACUC).  These results are a product of a consortium of researchers known as the Malaria Host Pathogen Interaction Center (MaHPIC).  For more information on the MaHPIC, please visit http://www.systemsbiology.emory.edu/ .  Within the MaHPIC, these data were collected as part of 'Experiment 04' (E04).  To access other publicly available results from E04 and other MaHPIC Experiments, including clinical results (specifics on drugs administered, diet, and veterinary interventions), and other omics data sets, please visit http://plasmodb.org/plasmo/mahpic.jsp .

first: Dalia

last: Arafat

first: Steve

last: Bosinger

first: Monica

last: Cabrera

first: Jeremy

last: DeBarry

first: Swetha

last: Garimalla

first: Jay

last: Humphrey

first: Ebru

last: Karpuzoglu

first: Jessica

last: Kissinger

first: Stacey

last: Lapp

last: Lee

first: Regina

last: Joice

first: Chet

last: Joyner

first: Esmeralda

last: Meyer

first: Alberto

last: Moreno

first: Vishal

last: Nayak

first: Mustafa

last: Nural

first: Suman

last: Pakala

first: Nirav

last: Patel

first: Yan

last: Tang

first: Greg

last: Tharp


title: Hormone responsive organoid cultures of human endometrium

status: Public on Apr 11 2017

city: Cambridge

first: Margherita

last: Turco

address: Department of Pathology, Tennis Court Road

department: Department of Pathology

institute: University of Cambridge

summary: Endometrial gland cultures were established from human non-pregnant endometrium and decidua. We analysed the global gene expression profile of the human endometrial gland organoid cultures to assess the similarity of their molecular signature to the tissue of origin. Organoid cultures established from decidua were also included in the analysis to assess their similarity to endometrial dervied cultures.

overall_design: For each tissue sample, the total RNA obtained from established organoids were used compared to both the initial glandular digests and stromal cells isolated from the same endometrial biopsy. Glands, Organoids and Stroma samples 1 to 7 refer to endometrial derived samples. Organoids 8 to 13 refer to decidua derived organoids.

middle: Y


title: Gene expression profile in stable RCAN1-4 knockdown thyroid cancer cell lines

status: Public on Apr 07 2017

city: Columbus

first: Lianbo

last: Yu

state: OH

address: 1800 Cannon Drive

department: Center for Biostatistics

institute: The Ohio State University

summary: To explore the effects of endogenous RCAN1-4 loss on thyroid cancer in vivo, we developed RCAN1-4 knockdown stable cells. Subcutaneous xenograft models demonstrated that RCAN1-4 knockdown promotes tumor growth. Intravenous metastasis models demonstrated that RCAN1-4 loss promotes tumor metastases to the lungs and their subsequent growth. Microarray was performed to understand how RCAN1-4 regulates tumor behaviors and the global effects of RCAN1-4 knockdown in these cells.

overall_design: Transcriptome data from two thyroid cancer cell lines: FTC236 and HTh74. For each cell lines, we developed RCAN1-4 knockdown stable cells (shRCAN1-4) using RCAN1-4 specific shRNA and control stable cells (shCtrl) using nontargeting shRNA. Three biological triplicates were used for each cell line.

first: Chaojie

last: Wang

first: Motoyasu

last: Saji

first: Steven

middle: E

last: Justiniano

first: Adlina

last: Mohd Yusof

first: Xiaoli

last: Zhang

first: Soledad

last: Fernández

first: Paul

last: Wakely Jr

first: Krista

last: La Perle

first: Hiroshi

last: Nakanishi

first: Neal

last: Pohlman

first: Matthew

last: Ringel


title: Genome-wide analysis of Su(var)3-9 distribution in chromosomes of Drosophila melanogaster

status: Public on Apr 04 2017

city: Novosibirsk

first: Petr

last: Laktionov

address: Lavrenitev ave 8/2

country: Russia

institute: Institute of molecular and cellular biology SD RAS

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Histone modifications represent one of the key factors contributing to proper genome regulation. One of the histone modifications involved in gene silencing is H3K9 methylation, which is found in the chromosomes across different eukaryotes and controlled by SU(VAR)3-9 and its orthologs. Although SU(VAR)3-9 was discovered over two decades ago, little is known about the details of its chromosomal distribution pattern. To fill in this gap, we used DamID-seq approach and obtained high-resolution genome-wide profiles for SU(VAR)3-9 in two somatic and two germline tissues of fruitfly.

overall_design: DamID-Seq profiling of Su(var)3-9 protein in somatic and germline cells of Drosophila melanogaster. We performed DamID profiling of Su(var)3-9 in male (M) and female (F) salivary glands (SG), larval brains (BR), germline nurse cells (NC) and at the different developmental stages of male germ cells, using testes of bam-, aly-, can-mutants and wild-type testes. For every experiment Dam-alone control was performed. Experiments were performed in replicates.

first: Daniil

last: Maksimov

first: Olga

middle: V

last: Posukh

first: Stepan

middle: N

last: Belyakin

first: Dmitry

last: Koryakov


title: Hormone-responsive organoid cultures of human endometrium

first: Margherita

last: Turco

summary:
The aim of the experiment was to investigate the effects of stimulation of human endometrial organoids with estrogen (E2) and progesterone (P4)
In humans, the endometrium, the uterine mucosal lining, undergoes dynamic changes throughout the menstrual cycle and in pregnancy.  We adapted conditions used to establish human adult stem cell-derived organoid cultures to generate 3D cultures of human endometrium. Unlike other mucosal epithelia, the endometrium responds dramatically to ovarian sex hormones, estrogen (E2) and progesterone (P4), which regulate cyclical proliferation and differentiation of endometrial glands with concomitant dynamic temporal and spatial expression of their receptors, ERalpha and PR.

overall_design: To mimic the response of the organoid cultures to hormones, we exposed them to E2 followed by P4 and performed a microarray analysis of organoids under the following conditions: ExM (control), E2 alone (E2)or E2 and P4 (E2P4).


title: BET N-terminal bromodomain inhibition selectively blocks Th17 cell differentiation and ameliorates colitis in mice

status: Public on Apr 01 2017

first: Rajal

last: Sharma

address: 1425 Madison Ave., Room 16-52

institute: ISMMS

summary: We analyzed the transcriptomic changes and Brd4 global occupancy in Th17 cells treated with JQ1 and MS402. We find that MS402 selectively targets Th17 cells and displaces Brd4 occupancy at Th17-selective genes.

overall_design: RNA-seq samples were analyzed from Th17 cells treated with JQ1 and MS402. ChIP-seq samples were analyzed to determine global Brd4 occupancy in response to MS402 treatement.

first: K

last: Cheung

first: M

last: Zhou


title: Genome-wide analysis of Su(var)3-9 distribution in chromosomes of Drosophila melanogaster [RNA-Seq_SuVar]

status: Public on Mar 30 2017

summary: One of the histone modifications involved in gene silencing is H3K9 methylation, which is found in the chromosomes across different eukaryotes and controlled by SU(VAR)3-9 and its orthologs. Although SU(VAR)3-9 was discovered over two decades ago, little is known about the details of its chromosomal distribution pattern and effect on gene regulation during germ cells development. To fill in this gap, we used RNA-Seq approach to investigate the effect of Su(var)3-9 mutation on gene expression during Drosophila spermatogenesis.

overall_design: RNA-Seq gene expression profiling in Su(var)3-9-mutant and wild-type testes of Drosophila melanogaster. Biological replicates were performed for each sample.


title: Novel physiological traits modulated by light in Acinetobacter baumannii assessed by whole transcriptome analysis.

status: Public on Mar 21 2017

city: Rosario

first: Alejandra

last: Mussi

state: Santa Fe

address: Suipacha 531

country: Argentina

institute: CEFOBI

summary: We have shown recently that in the human pathogen Acinetobacter baumannii, light is able to modulate key aspects contributing to its success as a pathogen such as motility, biofilm formation and virulence in a way that depends on the BLUF photoreceptor BlsA at 24ºC. In addition, light can induce reduction in susceptibility to certain antibiotics such as minocycline and tigecycline in a photoreceptor-independent manner, directly inducing expression of resistance genes. In this work, we performed RNAseq studies to identify new traits modulated by light in this pathogen in A. baumannii strain ATCC 19606. We have found 226 differentially expressed genes between light and dark, which comprise not only important determinants related to pathogenicity/resistance, but also to the bacteria´s survival in the environment.

overall_design: A. baumannii ATCC 19606 cells were exposed to blue light or incubated in the dark at 24C in LB in stagnant conditions overnight. RNA was extracted from these cells and the whole transcriptome was determined.

first: María

first: Gabriela

last: Müller

middle: S

last: Ramírez


title: Requirements for different Tcf1 isoforms in T cell development

status: Public on Mar 15 2017

city: Iowa City

first: Thomas

middle: B

last: Bair

state: IA

address: 335 EMRB

institute: University of Iowa

summary: Comparison of transcriptome between control, Tcf1 long isoform (p45)-deficient, complete Tcf1-deficient DN3 thymoctyes

overall_design: lineage-negative, CD4-, CD8-, CD44 low and CD25 high (DN3) thymocytes were sorted  from control mice or those are deficient for either Tcf1 long isoforms (p45) or all Tcf1 proteins. Lck-Cre was used to ablate all Tcf1 proteins

first: Hai-Hui

last: Xue


title: mRNA expression profiling of ebv-miR-BART7-expressing NPC cells

status: Public on Mar 31 2017

city: Hong Kong

first: Wei

last: Gao

address: 21 Sassoon Road

country: Hong Kong

institute: The University of Hong Kong

summary:
Nasopharyngeal carcinoma (NPC) is endemic in Southeast Asia and southern China. The primary treatment for NPC is radiotherapy. Despite of the encouraging results of radiotherapy, local recurrence or distant metastases of NPC after the initial therapy is frequently found due to radioresistance. Therefore, there is an urgent need to identify genes that control radiosensitivty, aiming to reduce disease recurrence. Epstein-Barr virus (EBV) infection was closely associated with undifferentiated NPC. EBV-encoded microRNAs (miRNAs) played crucial roles in the pathogenesis of NPC. Ebv-miR-BART7 belongs to the 44 EBV BART miRNAs and was found to be up-regulated in NPC tissues and plasma. Forced expression of ebv-miR-BART7 enhanced the radiosensitivity of NPC cells. However, the mechanisms underlying the sensitizing effect of ebv-miR-BART7 on radiation remain largely unknown.
Given that miRNA exerts biological functions by regulating its targets, we used microarray to identify the targets of ebv-miR-BART7 that regulate radiosensitivity of NPC cells.

overall_design: NPC HONE1 cells were transfected with ebv-miR-BART7 mimic or negative control siRNA. The experiment was done in duplicate. Then, HONE1 cells were irradiated at 4 gray. RNA were extracted and hybridized on Affymetrix microarrays.

first: Thian

last: Wong


title: ADAR1 controls apoptosis of stressed cells by inhibiting Staufen-mediated mRNA decay

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Both p150 and p110 isoforms of ADAR1 convert adenosine to inosine in double-stranded RNA (dsRNA).  The p150 isoform suppresses the dsRNA sensing mechanism that activates the interferon induction mediated by the MDA5-MAVS signaling.  In contrast, the biological function of the p110 isoform localized in the nucleus remains largely unknown. Here we show that stress-activated phosphorylation of ADAR1p110 by MKK6/p38 MAP kinases promotes its binding to Exportin-5 and nuclear export to the cytoplasm.  Once translocated to the cytoplasmic, ADAR1p110 suppresses apoptosis of stressed cells by protecting many anti-apoptotic gene transcripts that contain 3’UTR dsRNA structures such as those consisting of inverted Alu repeats.  ADAR1p110 competitively inhibits binding of Staufen1 to the 3’UTR dsRNAs and antagonizes the Staufen1-mediated mRNA decay mechanism.  Our studies revealed a new stress response mechanism regulated by MAP kinases, in which ADAR1p110 translocates to the cytoplasm and regulates a class of mRNAs required for survival of stressed cells.

overall_design: Examination of transcription changes due to ADAR1 and double ADAR1/STAU1 knockdown using RNA-seq

first: Kazuko

last: Nishikura

first: Masayuki

last: Sakurai


title: KDM1A confers invasive and metastatic attributes in lung adenocarcinoma by modulating a non-canonical Integrin ß3-KRAS signaling pathway

status: Public on Mar 13 2017

city: Cologne

first: Soyoung

last: Lim

address: Kerpener Str. 62

institute: Cologne medical school

summary: KRAS mutations occur in approximately 25% of non-small cell lung cancer (NSCLC). They account for the therapy resistance to EGFR inhibitors and are suggested to be difficult to target by specific drugs. Therefore, new therapies for KRAS mutant NSCLC are urgently needed. The histone H3K4 and H3K9 di/mono-demethylase KDM1A is a key epigenetic writer, aberrantly upregulated in many cancer types, including NSCLC. In order to understand the functional role of KDM1A in the progression of lung adenocarcinoma, KDM1A expression profiles were analysed in tissue microarrays (TMAs) including 182 lung adenocarcinoma. KDM1A expression correlated with high grade and metastasized tumor. To investigate the impact of KDM1A in lung adenocarcinoma development, we used the KRAS mutated A549 cell line to establish a shRNA-mediated stable KDM1A knockdown cell clone. Unexpectedly, KDM1A knockdown had only a slight effect on retardation of cell growth. However, cell invasion and self-renewal capability was significantly decreased by KDM1A inhibition. KDM1A knockdown in A549 cell resulted in a dramatic change in the transcriptome profile as determined by RNA-Seq. Interestingly, genes involved in the KRAS signature and lung epithelial marker genes were significantly affected upon KDM1A knockdown. Ingenuity pathway analysis also suggested that the alternative integrin β3-KRAS signaling axis, which is involved in stem cell like properties, is abrogated upon KDM1A knockdown. Indeed, Integrin β3 and its non-canonical ligand galectin-3 were strongly downregulated and their downstream NF-κB activity was decreased upon KDM1A knockdown. Finally, correlation of KDM1A to the Integrin β3 level was validated in TMAs.

overall_design: Determining the role of KDM1A in A549 cells, mRNA profiles of control and knockdown samples of A549 cells, generated by deep sequencing, in triplicate, using Illumina HiSeq 2500.

first: So-Young

first: Reinhard

last: Buettner

first: Michal

last: Schweiger

first: Margarete

last: Odenthal


title: Distinct roles of Brd2 and Brd4 in potentiating the transcriptional program for Th17 cell differentiation

first: Rajal

last: Sharma

summary: We analyzed the genome wide distributions of Brd2 and Brd4 in Th17 cells. We find that Brd2 and Brd4 have distinct genome-wide localization in Th17 cells, further experiments reveal tht Brd2 faciliates TF-complex formation in enhancers, enhancer-promoter interaction while Brd4 enhances transcriptional elongation.

overall_design: ChIP-seq study of Brd2 and Brd4 in Th17 cells. Additional samples include Brd4 and Brd2 ChIP-Seq after JQ1 treatment, as well as ChIP-seq of H3K4me1 and H3K27ac. The Th17 cells are differentiated for 48hrs and ChIP with the corresponding antibodies and ChIP-seq libraries are made.

first: K


title: Transcriptomic profiling of normal human cardiac fibroblast treated with halofuginone

status: Public on Mar 03 2017

city: Collegeville

first: Pu

last: Qin

address: 1250 S Collegeville Rd

institute: GSK

summary: Normal human cardiac fibroblast were treated with 200 nM halofuginone for 24 hours and the transcriptomic profile was measured by RNAseq.

overall_design: Total of 6 samples analyzed, 3 treated with vehicle and 3 treated with halofuginone.

first: Wendy

last: Halsey

first: Ashley

last: Hughes

first: Ganesh

last: Sathe

first: George

last: Livi

first: Xiaoyan

last: Qu

first: Deepak

last: Rajpal

first: Robert

last: Willette


title: Heterogeneity of hypothalamic Pro-opiomelanocortin-expressing neurons revealed by single-cell RNA sequencing

status: Public on Mar 08 2017

city: Box 289, Addenbrooke’s Hospital

first: Joseph

last: Polex-Wolf

state: Cambridgeshire

address: Wellcome Trust-MRC Institute of Metabolic Science

department: Metabolic Research Laboratories

summary: Arcuate proopiomelanocortin (POMC) neurons are critical nodes in the control of body weight. Often characterised simply as direct targets for leptin, recent data suggest a more complex architecture. Using single cell RNA sequencing, we have generated an atlas of gene expression in murine POMC neurons, and compare the gene expression profiles of individual POMC-expressing neurons to assess the degree of heterogenity present in this cell population.

overall_design: We isolated one hundred and sixty-three POMC-expressing neurons from the arcuate nucleus of POMC-EGFP transgenic mice using fluorescence activated cell sorting. RNA was extracted from individual neurons and subjected to RNA sequencing, after which the gene expression profiles of the individual Pomc-expressing neurons were compared.

first: Brian

last: Lam

first: Irene

last: Cimino

first: Giles

last: Yeo


title: Heme coordination and nitric oxide binding by Dnr regulators are essential for adaptation of Dinoroseobacter shibae to anaerobiosis

city: Braunschweig

first: Matthias

last: Ebert

address: Spielmannstraße 7

department: Institute of Microbiology

institute: Technical University Braunschweig

summary: The adaptation strategies and regulatory networks behind the adaptation of D. shibae DFL12T to nitrosative stress under anaerobic starvation was investigated. Furthermore, the role of the oxygen sensing regulator FnrL and the heme coordinating regulators DnrD and DnrF were determined under nitrosative stress conditions. Therefore transcriptional analyses were performed using regulator knock out strains.

sample_organism: Dinoroseobacter shibae DFL 12 = DSM 16493

overall_design: Dinoroseobacter shibae DFL12T (DSM 16493T) and corresponding fnrL, dnrD and dnrF depletion strains (DS001 (DfnrL), DS002 (DdnrD) and DS004 (DdnrF)) were grown in artificial saltwater minimal medium (SWM) supplemented with 16.9 mM succinate in baffled flasks shaking at 200 rpm for aerobic growth and for anaerobic cultivation 25 mM pyruvate was added and incubation was performed in serum flasks with rubber stoppers shaking a 100 rpm. For nitrosative stress conditions 50 nM of NO saturated water was added. D. shibae wild type and mutant strains were grown under aerobic conditions up to the mid exponential growth phase (OD578 nM 0.5) and shifted to anaerobiosis to mimicke the physiologic conditions in the marine habitat. The samples were taken before (as reference) NO injection and after 30 minutes of nitrosative stress. Three biological replicas were analyzed. Comparison: Identification of genes induced or repressed in the Dinoroseobacter shibae DSM 16493T Crp/ Fnr regulator mutant strains and wild type strain the under nitrosative stress conditions.

first: Peter

last: Schweyen

first: Martin

last: Bröring

first: Sebastian

last: Laaß

first: Elisabeth

last: Härtig

first: Dieter

last: Jahn


title: Genomewide analysis of EGF-induced alternative splicing

status: Public on Mar 01 2017

city: Shanghai

first: Feng

last: Wang

state: Shanghai

address: Yueyang Road 320

department: State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science

country: China

institute: Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

summary: We performed EGF treatment and hnRNP A1 knockdown in HeLa cells and analyzed alternative splicing patterns by high-throughput RNA sequencing.

overall_design: The mRNA profiles of control/EGF-treated/hnRNP A1-knockdown HeLa cells were generated by deep sequencing using Illumina HiSeq2000.

first: Jingyi

last: Hui

first: Xing

last: Fu


title: Identification of mesothelial-to-mesenchymal gene signature in ascitic fluid-isolated mesothelial cells through RNA-sequencing

city: Houston

first: Chi Lam

last: Au Yeung

state: TX

address: 1515 Holcombe Blvd

institute: UT MD Anderson Cancer Center

summary: RNA-sequencing analysis was carried out on ascetic fluid-isolated mesothelial cells from ovarian cancer patients compared to control human peritoneal mesothelial cells to identify a mesothelial-mesenchymal gene signature.

overall_design: Three control human peritoneal mesothelial cell samples isolated from omentum obtained from non-oncologic patients undergoing abdominal surgery and three ascitic fluid-isolated mesothelial cell samples obtained from the peritoneal effucsions of stage III/IV ovarian serous carcinoma patients

first: Angela

last: Rynne-Vidal


title: Differential transcrpitome analysis of Sertoli cells during their phases of postnatal maturation in rat testes

city: New Delhi

first: Subeer

last: Majumdar

state: Delhi

address: Aruna Asaf Ali Marg, JNU Complex

country: India

institute: National Institute of Immunology

summary: Spermatogenesis is a complex process involving multiple cells and cellular signals. Among all other cells, Sertoli cells (Sc) are absolutely indispensable for sperm production because they provide biochemical signal and physical support to developing germ cells in the testis. Sc drastically transform during the process of attainment of reproductive maturity. Stage specific gene expression by Sc, supplement for the changing need of developing germ cells. A conspicuous absence of comprehensive gene expression data from various stages of developing Sertoli cells hinders our knowledge of regulating inputs necessary for the process of spermatogenesis.

overall_design:
We have compared genome wide expression of genes among 5 days, 12 days and 60 days old Sc.
Agilent one-color experiment, Agilent Whole Genome Rat  4x44k  (AMADID: 014879), Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

first: Mukesh

last: Gautam

first: Indrashis

last: Bhattacharya


title: Expression data from mouse skin cell lines in various stages of tumorigenesis

city: San Francisco

first: Kyle

last: Halliwill

address: 1450 Third Street

department: Helen Diller Family Comprehensive Cancer Center

institute: UCSF

summary:
Mouse skin cell lines in various stages of tumorigenesis were assayed for transcriptome-wide expression levels.
We assessed gene expression levels in mouse skin cell lines representing immortalized keratinocytes, premalignant lesions, malignant squamous cell carcinomas, and malignant squamous cell carcinomas with spindle morphology. These tumors were overwhelmingly driven by Hras mutations. The cells themselves were derived from multiple mouse strains.

overall_design: We grew cells in serum supplemented media. RNA was harvested from log-phase cells by Qiagen kit and hybridized to Affymetrix M430 2.0 arrays.

first: Allan

last: Balmain


title: RNA sequencing of CDH1+/THY1+ and CDH1-/THY1+ germline stem cells

city: Bloomington

first: Aaron

last: Buechlein

state: IN

address: 1001 E 3rd St

department: Center for Genomics and Bioinformatics

institute: Indiana University

summary: To futher understand the properties of CDH1+ GSCs and CDH1- GSCs, flow cytometry was used to sort the twopopulations after trypsin digestion and they were compared by total RNA sequencing (RNA-seq). The data clearlyshowed CDH1+ and CDH1- cells as having highly distinct profiles. In particular, numerous epithelial genes (e.g.Dsp, Pkp2, Krt19) were highly expressed in the CDH1+ population. In contrast, most genes known to be generalmarkers of SSCs/undifferentiated spermatogonia were downregulated (e.g. GFRA1 and ID4) or unchanged (e.g. ZBTB16and SALL4) in CDH1- GSCs. Additionally, KEGG pathway analysis revealed that the two populations exhibiteddistinctive activity in several signaling pathways including WNT and TGFb signaling. Notably, Tgfbr1, Smad2, Smad3tended to be lower in CDH1+ GSCs while Smad7, an inhibitor of TGFb signaling, was higher.The results showed thatCDH1+ GSCs were more epithelial in nature compared to CDH1- GSCs and supported the notion that CDH1+ GSCs are areable to partly overcome MET barrier because they may be in an advanced stage of MET.

overall_design: Examination of RNA levels in CDH1+/THY1+ and CDH1-/THY1+ GSCs.

first: Christina

middle: T

last: Dann

first: Junhui

last: An


title: Microarray Profiling of Circular RNAs in Human Papillary Thyroid Carcinoma

status: Public on Feb 23 2017

city: Guiyang

first: Nianchun

last: Peng

state: Guizhou

address: No. 9 Beijing road, Yunyan district, Guiyang, Guizhou, China

department: Endocrinology and Metabolism

institute: Affiliated Hospital of Guizhou Medical University

summary: Background: Non-coding circular RNAs (circRNAs) have displayed dysregulated expression in several human cancers. Here, we profiled the circRNA expression of papillary thyroid carcinoma (PTC) tumors to improve our understanding of PTC pathogenesis as well as to identify potential circRNA biomarkers for PTC.

overall_design: A total of 18 thyroid samples – consisting of six PTC tumors, six matching contralateral normal samples, and six benign thyroid lesions (i.e., three follicular adenoma samples and three multinodular goiter samples) – were finally included in the study.

first: Lixin

last: Shi


title: Expression data of HBV infected liver tissue

status: Public on Feb 28 2017

city: Ann Arbor

first: Weichen

last: Zhou

state: Michigan

address: 800 fuller St. 26

institute: Fudan University

summary: We analyzed three clinical parameters with gene expression data from 122 liver tissues. Six healthy samples were used in validation.

overall_design: All hepatitis samples were HBV infected, which was validated by positive HBsAg or serum HBV-DNA. The samples with HCV infection or metabolic liver injury (e.g. fatty liver, chronic alcoholic hepatitis, etc.) were excluded.

first: Yanyun

last: Ma

first: Jiucun

first: Hongyuan

last: Zheng

first: Jie

last: Liu


title: Genome-wide identification of small RNAs expressed in multidrug-resistant Enterococcus faecium and their implications in daptomycin resistance

status: Public on Feb 16 2017

city: Rennes

first: Vincent

last: Cattoir

address: 2 rue Henri Le Guilloux

institute: CHU de Rennes

summary: Regulatory RNAs (sRNAs) are now considered as major players in many physiological and adaptive responses in pathogenic bacteria. sRNAs have been extensively studied in Gram-negative bacteria, but less information is available in Gram-positive pathogens. There is a spread of multidrug-resistant (MDR) opportunistic organisms, grouped as “ESKAPE” pathogens, which comprise enterococci, a leading cause of hospital-acquired infections and outbreaks with emergence of MDR isolates, especially vancomycin-resistant Enterococcus faecium (VREF). Note that no information about sRNA expression is known in this major opportunistic pathogen. By transcriptomic and genomic analyses using E. faecium Aus0004 reference strain, 249 transcribed IGRs, including sRNA candidates, were detected and, using a series of cut-offs, this set was lowered down to 54 sRNAs while 7 that were predicted based on comparative sequence analysis. RNA-seq was performed with and without subinhibitory concentrations (SIC) of daptomycin, a cyclic lipopeptide antibiotic used for VREF infections. Under daptomycin SIC exposure, 260 genes (9.1% of the genome) had a significant alteration of expression including 80 upregulated genes and 180 downregulated genes. Among the repressed genes, a large proportion (55%) coded for proteins involved in carbohydrate and transport metabolism. Also, we focused on the 9 sRNAs exhibiting the highest expression, and all of them were confirmed as expressed along bacterial growth by Northern blots and qPCR. Out of these 9 sRNAs, four had significantly lower or higher expression in the presence of daptomycin SIC, and therefore responded to antibiotic exposure. Finally, we also tested the expression of these 9 sRNAs in a collection of isogenic Aus0004 mutants with increasing levels of daptomycin resistance, and we observed by qPCR that some sRNAs had a significantly modified expression in daptomycin resistance mutants. It highlights the significant implication of some of the E. faecium sRNAs in the early steps of the development of daptomycin resistance. This is the first experimental genome-wide sRNA identification in Gram-positive E. faecium, a leading cause of hospital acquired infections.

overall_design: Identification of the first sRNAs in Enterococcus faecium and transcriptome analysis by RNA-seq to monitor the levels of all transcripts (mRNAs and sRNAs) in bacterial cells grown in the absence or the presence of a subinhibitory concentration (0.5 mg/L) of daptomycin

first: Clara

last: Sinel

first: Yoann

last: Augagneur

first: Mohamed

last: Sassi

first: Brice

last: Felden


title: Expression data from Drosophila larvae

status: Public on Feb 09 2017

city: Kanazawa

first: Takayuki

last: Kuraishi

address: Shizenken, Kakuma-machi

institute: Kanazawa University

summary:
The expression of Drosomycin, an antimicrobial peptide, is induced by pinching larvae with forceps in Drosophila
We used microarray to examine whether other innate immune genes are up-regulated upon pinching.

overall_design: Drosophila larvae were pricked with tungsten needle or pinched by forceps, incubated for 4 hours, and subjected to RNA extraction and hybridization on Affymetrix microarrays.

first: Aki

last: Hori


title: A genome-wide analysis of human pluripotent stem cell-derived endothelial cells cultured in synthetic hydrogels compared to standard 2D or 3D cell culture platforms

status: Public on Feb 22 2017

city: Madison

first: Scott

last: Swanson

state: WI

address: 330 N. Orchard St

institute: Morgridge Institute for Research

summary: The influence of 2D and 3D cell culture platforms on vascular function was investigated by comparing gene expression for human pluripotent stem cell-derived endothelial cells (H1-ECs), primary human brain vascular pericytes (pericytes), and human umbilical vein endothelial cells (HUVECs) cultured on tissue culture polystyrene (TCP, “2D”), on or in poly(ethylene glycol) (PEG) hydrogels formed via “thiol-ene” photopolymerization, and on or in gelled Matrigel.  ECs cocultured with pericytes in PEG formed vascular networks with global gene expression that was highly correlated to a standard 3D Matrigel assay (Spearman’s coefficients ≥ 0.98).  H1-ECs, HUVECs, and pericytes  were characterized gene expression signatures associated with the cell cycle and mitosis when cultured on TCP surfaces compared to cells cultured on top of or encapsulated in PEG hydrogels or Matrigel. The proliferative signature was not necessarily a function of the 2D format, since endothelial cells cultured on PEG hydrogels were not characterized by increased proliferation or a proliferative gene signature compared to cells encapsulated in PEG hydrogels. The proliferative phenotype for H1-ECs on TCP was regulated by FAK-ERK activity, and inhibition or knockdown of ERK pathway signaling decreased proliferation and cell cycle genes while increasing expression of “3D-like” vasculature development genes.  Our results suggest that cells in 2D culture adopt a highly proliferative state that interferes with normal vascular function and provides unique insight into the importance of cellular and extracellular context for in vitro tissue modeling.

overall_design:
30 samples for RNA-Seq Experiment #1 ("RNAseq1": H1 human embryonic stem cells, “H1-ESC-1”; H1 ES cells-derived endothelial cells, "H1-EC1"; HUVECs, "HUV1"; pericytes, "PC"; and H1-EC1 cocultured with PC, H1-EC1-PC cocultures). Poly(ethylene glycol) (PEG) hydrogels : 4 million endothelial cells/mL (H1-EC1 or HUVECs) and/or 2 million pericytes/mL were encapsulated in 30 µL PEG hydrogels in the bottom of 24-well transwell inserts . Matrigel (MG): 2 million endothelial cells/mL and 1 million pericytes/mL were encapsulated in 30 µL gelled Matrigel (4.5 mg/mL). Endothelial cells, pericytes, and cocultures encapsulated in PEG or Matrigel were maintained under hypoxic conditions (1.5% O2) in E7V medium supplemented with 1% bovine serum albumin.  H1-ECs were also seeded on gelled Matrigel (4.5 mg/mL, “2D on Matrigel”) at a density of 60,000 cells/cm2 and incubated for one day in E7V medium with 1% BSA under normoxic conditions.  Tissue culture polystyrene (TCP): TCP surfaces were coated with Matrigel at a dilute concentration that does not form a gel (H1-ES cells), recombinant vitronectin (H1-ECs or HUVECs), or poly-l-lysine (pericytes, as per manufacturer’s instructions) and cultured under normoxic conditions.
18 samples for RNA-Seq Experiment #2 ("RNAseq2": H1-ECs, “H1-EC2”; or HUVECs “HUV2”; cultured using PEG hydrogels, gelled Matrigel (6.4 mg/mL), or on Matrigel-coated TCP surfaces.  For 3D culture, 4 million endothelial cells/mL were encapsulated in 30 µL PEG hydrogels (50% crosslinking, 2 mM CRGDS) or gelled Matrigel formed in single wells of 24-well TCP plates. For 2D culture, 200,000 endothelial cells per well of a 12-well TCP plates were seeded on Matrigel-coated surfaces (“MG-TCP”) or on 300 µL PEG hydrogels (50% crosslinking, 2 mM CRGDS) or gelled Matrigel formed in the bottom of the well. H1-ES cells were included as a control for both experiments. Duplicate samples are provided for each condition.

first: Jue

last: Zhang

first: Michael

last: Schwartz


title: Converting adult pancreatic α-cells into β-cells by targeting Dnmt1 and Arx

city: Stanford

first: Martin

last: Enge

address: James H. Clark Center, 318 Campus Drive,

department: Bioengineering

institute: Stanford University

summary: After their destruction in adult mice, insulin-producing pancreatic beta-cells slowly regenerate from other islet cells, like glucagon-producing alpha-cells. However the molecular basis of this conversion is unknown. Moreover it remains unclear if this intra-islet cell conversion is relevant to human diseases with extensive beta-cell loss, like in type 1 diabetes (T1D). Here, we show that subsets of glucagon-expressing cells in subjects with T1D produce Insulin and other molecular features of beta-cells, accompanied by loss of the alpha-cell regulators DNA methyltransferase 1 (Dnmt1) and Aristaless-related homeobox (Arx). We generated mice permitting lineage tracing and inactivation of Dnmt1 and Arx in adult alpha-cells. Within 3 months of Dnmt1 and Arx loss, 50% of alpha-cells converted into cells producing insulin protein but not glucagon, changes not observed in alpha-cells after only Arx or Dnmt1 loss. Single cell isolation and high-throughput RNA sequencing revealed efficient and extensive alpha-cell conversion into progeny indistinguishable by global gene expression from native beta-cells. Our work reveals pathways regulated by Arx and Dnmt1 sufficient for achieving targeted generation of beta-cells from adult pancreatic alpha-cells.

overall_design: Single-cell RNA-seq of in-vivo conversion of pancreatic α-cells into β-cells

first: Harini

last: Chakravarthy


title: Role of the Dickeya dadantii PecS regulator during the early stages of plant infection

status: Public on Feb 10 2017

city: Paris

first: Jacques

last: Pédron

address: 4 place Jussieu

department: Biology

institute: Université Pierre et Marie Curie

summary: Investigation of whole genome gene expression level changes during plant infection in the PecS regulatory mutant compared to the wild type strain.  PecS is a global regulator of virulence in D. dadantii and the PecS mutant is hypervirulent.

overall_design: Microarray study using total RNA extracted from bacteria purified out of Arabidopsis leaf material. Each chip measures the expression level of 4,753  genes from D. dadantii 3937.

first: Frédérique

last: Van Gijsegem


title: Defective Decidualization During and After Severe Preeclampsia Reveals a Possible Maternal Contribution to the Etiology

status: Public on Feb 08 2017

city: SAN FRANCISCO

first: Susan

last: Fisher

address: 513 PARNASSUS AVE

department: Obstretrics, Gynecology and Reproductive Sciences

summary: In preeclampsia (PE), cytotrophoblast (CTB) invasion of the uterus and spiral arteries is often shallow. Thus, the placenta’s role has been a focus. We hypothesized that decidual defects are an important determinant of the placental phenotype. We isolated (human) endometrial stromal cells (hESCs) from non-pregnant donors with a prior pregnancy that was complicated by severe PE (sPE). Versus controls, they failed to decidualize as demonstrated by morphological criteria and the analysis of stage-specific antigens. These results were bolstered by showing that they were transcriptionally inert. Additionally, we used laser microdissection to isolate the decidua from tissue sections of the maternal-fetal interface. Transcriptional profiling revealed sPE-associated defects in gene expression. Also, decidual cells from sPE patients, which de-differentiated in vitro, failed to re-decidualize in culture. Immediately following isolation they released factors that inhibited CTB invasion, linking a possible cause to a known effect. These data suggested that failed decidualization is an important contributor to down regulated CTB invasion in sPE. Diagnosis of this defect prior to pregnancy would enable therapies that are designed to improve decidualization, a novel strategy for prevention.

overall_design: We used laser microdissection to isolate the decidua basalis and parietalis from sPE and nPTB samples (n=4/ group). Biopsies of the placenta/decidua basalis and smooth chorion/decidua parietalis were washed repeatedly in cold PBS to remove blood contaminants then placed in cryomolds containing OCT, frozen over a dry ice/ethanol slurry, and stored at -80C.

first: T

last: Garrido-Gomez

first: F

last: Dominguez

first: A

last: Quiñonero

first: P

last: Diaz-Gimeno

first: K

last: Ona

first: M

last: Kapidzic

last: Gormley

last: Padilla

last: Perales

first: O

last: Genbacev

first: C

last: Simón

first: S


title: miRNA expression in nephron progenitors of the developing kidney

status: Public on Feb 01 2017

city: Pittsburgh

first: Jacqueline

last: Ho

address: 4401 Penn Avenue

department: Pediatrics

institute: Children's Hospital of Pittsburgh

summary: mIRNA expression profiling of mouse embryonic nephron progenitors at embryonic day 14 isolated by GFP expression driven by Six2-TGC (transgenic mouse line), compared to whole embryonic kidney at day 14

overall_design: Two types of sample (nephron progenitors versus whole embryonic kidney); three biological replicates for each independently isolated for nephron progenitors ( pooled from 6-7 embryonic kidneys in one litter) compared to one E14 kidney


title: Genome-wide RNA expression analysis of rat dorsal root ganglion tissue after local absorbable collagen sponge implantation and BMP-2 exposure

status: Public on Jan 27 2017

city: Bethesda

first: Clifton

middle: Lee

last: Dalgard

state: Maryland

address: 4301 Jones Bridge Road B2038

department: Anatomy Physiology & Genetics

institute: Uniformed Services University

summary: Analysis of whole dorsal root ganglion tissue expression signatures in responses to absorbable collagen sponge implantation with and without BMP-2 exposure.  The hypothesis is that inflammatory macrophage-associated responses to ACS implantation contributes to nociception in the DRG and spinal nerve.

overall_design: Total RNA obtained from recipient rat dorsal root gangion tissue at days 1, 3 and 7 post-implantation were profiled by Illumina BeadArray expression analysis

first: Aviva

last: Symes


title: Regenerating Zebrafish fins: Controls vs. regenerating fins (3 days following fin amputation)

city: PESSAC

first: Abdel-Majid

last: Khatib

address: av des Facultes

institute: INSERM

summary: Transcriptional profiling of zebrafish rergenerating fins comparing control fins and regenerating fins (3 days following fin amputation)

overall_design: Two-condition experiment, normal fins vs. regenerating fins (3 days following fin amputation)

first: Geraldine

last: Siegfried


title: Possible roles of CC- and CXC- chemokines in regulating bovine endometrial function during early pregnancy

status: Public on Jan 14 2017

city: Morioka

first: Keiichiro

last: Kizaki

state: Iwate

department: Vet. Med.

institute: Iwate University

summary: The aim of the present study is to determine possible roles of chemokines in regulating bovine endometrial function during early pregnancy. A 15 K bovine oligo DNA microarray detected 344 and 1336 differentially expressed genes (>2-fold; P<0.05) in the bovine endometrium of 15 and 18 days of pregnancy compared with these days of the estrous cycle (cyclic, n=4). The expression of six chemokines, including CCL2, CCL8, CCL11, CCL14, CCL16 and CXCL10 was higher in the endometrium of early pregnancy than that in the cyclic stage.

overall_design: Bovine uteri were obtained from Japanese-Black cows in the institute ranch within 10-30 min of exsanguination. Tissue samples were collected from cows on 15 and 18 days of the estrous cycle (NP15 and NP18) and the gestation (P15 and P18)(n=4 animals/each day). The day of artificial insemination was designated as day 1.

first: Ryosuke

last: Sakumoto


title: Population STARR-seq in preadipocytes pre/post differentiation

city: Durham

first: Timothy

last: Reddy

state: NC

address: 101 Science Dr. RM 2383

institute: Duke University

summary: Transversions (Tv's) are more likely to alter the amino acid sequence of proteins than transitions (Ts's), and local deviations in the Ts:Tv ratio are indicative of evolutionary selection on genes. Whether the two different types of mutations have different effects in non-protein-coding sequences remains unknown. Here, we provide multiple lines of evidence demonstrating that Tv’s have larger impacts on regulatory DNA including analyses of transcription factor (TF) binding motifs, allele-specific TF binding, and genome-wide Tv density within accessible chromatin. Using massively parallel population-scale reporter assays, we also provide empirical evidence that Tv's have larger effects than Ts's on the activity of human gene regulatory elements. Understanding the features of functional non-coding variation will be valuable for revealing the genetic underpinnings of complex traits and diseases.

overall_design: STARR-seq libraries were generated from captured open chromatin regions at 3q25 in 760 individuals and transfected into HepG2 cells.

first: Cong

last: Guo

first: Ian

last: McDowell

first: Michael

last: Nodzenski

first: Denise

middle: M

last: Scholtens

first: William

last: Lowe


title: Circulating plasma microRNA profiling in patients with polymyositis/dermatomyositis before and after treatment

status: Public on Feb 07 2017

city: Urayasu-Shi

first: Takuya

last: Hirai

state: Chiba

address: 2-1-1, Tomioka

institute: Juntendo University Urayasu Hospital

summary:
This study aimed to investigate the expression of microRNAs (miRNAs) in the plasma from polymyositis (PM) and dermatomyositis (DM) patients, which fluctuated by treatment.
More differentially expressed miRNAs were found in plasma of DM patients compared to PM patients before and after treatment, and their profiles were different.

overall_design: Total RNA was isolated from plasma of PM/DM patients before and after treatment with prednisolone, or, in case of prednisolone resistance or complications, with the combination of calcineurin inhibitors (cyclosporine or tacrolims) and/or pulse intravenous cyclophosphamide.

first: Iwao

last: Sekigawa


title: RNA-Seq analysis of E15.5 pancreas of both whole body Nkx2.2 mutant embryos and endocrine progenitor specific Nkx2.2 mutant embryos

status: Public on Jan 09 2017

city: Aurora

first: Lori

last: Sussel

state: CO

address: 1775 Aurora Ct.

institute: University of Colorado

summary:
Aim: Transcriptional analysis of E15.5 whole pancreas of Nkx2.2-LacZ/LacZ embryos versus control and Ngn3-Cre; Nkx2.2-flox/flox embryos versus control
Methods: Embryonic pancreata were isolated at E15.5 from Nkx2.2 mutant mice and controls. Total RNA was extracted. Libraries were prepared from total RNA (RIN>8) with the TruSeq RNA prep kit (Illumina) and sequenced using the HiSeq2000 (Illumina) instrument. More than 20 million reads were mapped to the mouse genome (UCSC/mm9) using Tophat (version 2.0.4) with 4 mismatches and 10 maximum multiple hits. Significantly differentially expressed genes were calculated using DEseq.
Results: There is significant overlap between the differentially expressed genes of whole body Nkx2.2 mutant embryos and endocrine progenitor specific Nkx2.2 mutant embryos; many of the downregulated genes (p-value < 0.05) are genes involved in beta cell function.
Conclusion: Nkx2.2 functions within the endocrine progenitor lineage to activate beta cell genes

overall_design: mRNA profiles of whole embryonic pancreata of E15.5 Nkx2.2 mutant and control embryos were generated by deep sequencing, in triplicate, using Illumina HiSeq2000.

first: Angela

last: Churchill

middle: G


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

status: Public on Jan 10 2017

city: Beijing

first: qu

last: lili

address: No 8 East Road, Fengtai District

institute: Affiliated Hospital of the Academy of Military Medical Science

summary: To identify a plasma miRNA panel that could help to separate NSCLC patients with EGFR sensitive mutations and wild-type EGFR, plasma samples of 3 EGFR19DEL, 3 EGFRp.L858R, and 3 EGFRWT patients with NSCLC and 4 HCs were selected for Agilent miRNA microarray analysis to detect differences in the expression levels of circulating miRNAs (n = 2,568) between the above cohorts.

overall_design: In the study presented here, plasma samples of 3 EGFR19DEL, 3 EGFRp.L858R, and 3 EGFRWT patients with newly diagnosed NSCLC and 4 HCs were selected for the Agilent microRNA array expression profiles with a total of 2.568 unique miRNAs. The significantly dysregulated miRNAs between the above cohorts were then validated by qRT-PCR.

first: Xiaoqing

last: Liu

first: Lili

last: Qu


title: FnrL and three Dnr regulators are used for the metabolic adaptation to low oxygen tension in Dinoroseobacter shibae

status: Public on Jan 17 2017

city: Braunschweig

first: Matthias

last: Ebert

address: Spielmannstraße 7

institute: Technical University Braunschweig

summary: The adaptation strategies and regulatory networks behind the adaptation of D. shibae DFL12T to changing oxygen regimes was investigated. Moreover, the essential role of 4 Crp/ Fnr like regulators within this adaptation process was revealed using transcriptional analysis of regulator knock out strains.

platform_organism: Dinoroseobacter shibae DFL 12 = DSM 16493

overall_design: Dinoroseobacter shibae DFL12T (DSM 16493T) and generated Crp/ Fnr regulator depletion strains (DS001 (DfnrL), DS002 (DdnrD), DS003 (DdnrE) and DS004 (DdnrF)) were grown in artificial saltwater minimal medium (SWM) supplemented with 16.9 mM succinate in baffled flasks shaking at 200 rpm for aerobic growth and for anaerobic cultivation 25 mM nitrate was added and incubation was performed in serum flasks with rubber stoppers shaking a 100 rpm. D. shibae wild type and mutant strains were grown under aerobic conditions up to the mid exponential growth phase (OD578 nM 0.5) and shifted to anaerobiosis to mimicke the physiologic conditions in the marine habitat. The samples were taken before (as reference) shift and 60 minutes after the shift. Three biological replicas were analyzed. Comparison: Identification of genes induced or repressed in the Dinoroseobacter shibae DSM 16493T Crp/ Fnr regulator mutant strains and wild type strain under changing oxygen regimes.

first: Sebastian

last: Laaß

first: Denitsa

last: Eckweiler

first: Louisa

last: Roselius

first: Andrea

last: Thürmer

first: Rolf

last: Daniel

first: Elisabeth

last: Härtig

first: Dieter

last: Jahn


title: Defective Decidualization During and After Severe Preeclampsia

first: Susan

last: Fisher

state: CA

institute: UCSF

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

overall_design: Refer to individual Series


title: Translatome analysis of NB-LRR immune response identifies important contributors to plant immunity in Arabidopsis.

status: Public on Mar 06 2017

city: Sherbrooke

first: Jean-Francois

last: Lucier

state: Quebec

address: 2500, boulevard de l'Université

department: Département de Biologie

country: Canada

institute: Université de Sherbrooke

summary: An important branch of plant immunity involves the recognition of pathogens by the NB-LRR proteins encoded by disease resistance genes. However, signaling events downstream of NB-LRR activation are poorly understood. We have analyzed the Arabidopsis translatome using ribosome affinity purification and RNAseq. Our results show that the translational status of hundreds of genes are differentially affected upon activation of the NB-LRR protein RPM1, showing an overall pattern of a switch away from growth-related activities to defense. Among these is the central translational regulator and growth promoter, TOR kinase. Suppression of TOR expression leads to increased resistance to pathogens while overexpression of TOR results in increased susceptibility, indicating an important role for translational control in the growth to defense switch. Furthermore, we show that several additional genes whose mRNAs are translationally regulated, including BIG, CCT2 and CIPK5, are required for plant innate immunity, identifying novel actors in plant defense.

overall_design: Cellular extracts of Arabidopsis Avr/L18 at 2h after spraying with DEX (30μM) or water (control) were prepared for ribosome IP followed by RNA purification. Total RNA from the same samples was purified in parallel. NGS libraries were prepared in biological triplicate for each treatment and RNA fraction (total and ribosome IP). Sequencing was performed on an Illumina HiSeq 2000 system at the Broad Institute of Massachusets Institute of Technology. Total RNA and ribosomebound mRNAs libraries were pairedend sequenced on two independent sequencing lanes as multiplexed samples. Raw demultiplexed fastq files are provided for each replicate. After checking the quality of the raw reads using FastQC (v0.10), reads were aligned on the TAIR10 assembly of A. thaliana Col0 genome using TopHat (v2.0.8) with default parameters "q10". CuffDiff (v2.1.1) was then used with parameters fragbiascorrect, multireadcorrect and the genome annotations file from NCBI 20130306 to identify differentially expressed genes at the level of translation ('HR1_vs_control_1_gene_exp,) and at the level of transcription ('HR2_vs_control_2_gene_exp'). In both processed data files, sample 1 stands for control and sample 2 for DEX.

first: Louis-Valentin

last: Meteignier

first: Mohamed

last: Oirdi

first: Mathias

last: Cohen

first: Teura

last: Barff

first: Dominick

last: Matteau

first: Jean-François

first: Pierre-Etienne

last: Jacques

first: Sébastien

last: Rodrigue

first: Keiko

last: Yoshioka

first: Peter

last: Moffett


title: Genome-wide SNP Profiling of 27 Neuroblastoma Cell Lines

city: Philadelphia

first: Jo Lynne

last: Rokita

address: 3501 Civic Center Blvd

institute: Children's Hospital of Philadelphia

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

summary: We used SNP arrays to perform genome-wide profiling of commonly-used neuroblastoma cell lines.

overall_design: Cells were cultured, pelleted, and DNA was extracted as below. DNA was used according to the manufacturer's guidelines in a genome-wide SNP array.

first: JoLynne

last: Harenza

first: Maura

last: Diamond

first: John

last: Maris


title: Differentially expressed genes after miRNA or siRNA transfection in human cancer cell lines (A-498, 786-O, A549, TE-8, PANC-1, SW1990, PC3 and PC3M)

status: Public on Jan 08 2017

city: Chiba

first: Naohiko

last: Seki

address: 1-8-1, Inohana

department: Functional Genomics

institute: Chiba University

summary: To identify differentially expressed genes by anti cancer treatments (microRNAs or siRNAs) in human cancer, several cell lines ( renal cell carcinoma, lung adenocarcinoma, esophageal, pancreatic and prostate cancer) were subjected to Agilent whole genome microarrays.

overall_design: Human cell lines (A-498, 786-O, A549, TE-8, PANC-1, SW1990, PC3 and PC3M) were treated with miRNAs (miR-10a-5p, miR-150-5p, miR-150-3p, miR-148a-5p, miR-148a-3p, miR-499a-5p, miR-455-3p and miR-455-5p), siRNAs (si-ANLN).

first: Takayuki

last: Arai


title: UHRF1 is an upstream regulator of DNMT1-mediated cellular senescence

status: Public on Jan 20 2017

city: Suwon

first: Hyun Goo

last: Woo

address: 164 Worldcup-ro Yeongtong-gu

country: South Korea

institute: Ajou University School of Medicine

summary: During the progress of senescence, cells sequentially acquire diverse senescent phenotypes together with several gene reprogramming steps. It is still unclear what will be the key regulator in charge of collective gene expression changes at the initial senescent reprogramming. In this study, we show that suppression of DNA methyltransferase 1 (DNMT1)-mediated maintenance DNA methylation activity was an initial event developed prior to gain of senescent phenotypes by employing time-series gene expression profiles of two different senescence models of human diploid fibroblast (HDF), replicative senescence (RS; GSE41714) and H2O2-induced senescence (HS).

overall_design:
The analysis of gene expression profiling among cellular senescence induced by hydrogen peroxide.
two different data sets; a sample set of senescence by H2O2 (n =7 including control sample) and a set of siRNA-mediated knockdown experiment (n=5 including control sample).

first: H

last: WOO

first: G

last: YOON


title: RNAseq analysis of FACs sorted E-cadherin+,  Kit+ and K5-venus+ cells from E15 K5-venus mouse submandibular salivary glands

status: Public on Jan 01 2017

first: Matthew

last: Hoffman

state: MD

address: 30 Convent Dr MSC4370

institute: NIDCR

summary: We used embryonic day 15 submandibular salivary glands from K5-Venus mice, which were produced using the bovine-K5 promoter driving Venus expression, N=3 separate experiments

overall_design: Anti-E-cadherin APC (FAB7481A, R&D Systems) and anti-Kit PE (BD Biosciences) were also used to FACs sort the cells.  Total RNA was extracted from epithelial cells sorted by FACS analysis and RNAseq performed by Cofactor Genomics (www.cofactorgenomics.com). Single-ended reads (50 nt in length) were produced using Illumina sequencer (Illumina).


title: Epigenetic Modifiers Facilitate Induction and Pluripotency of Porcine iPSCs

status: Public on Jan 06 2017

city: Hangzhou

first: Jian

last: Mao

address: 2318 Yuhangtang Rd

institute: Hangzhou Normal University

summary: Inadequate silence of exogenous genes represents a major obstacle to complete epigenetic reprogramming of pig induced pluripotent stem cells (piPSCs) by conventional pluripotency trasncription factors. We tested the hypothesis that epigenetic modification by active DNA or histone demethylation or by inhibition of histone deacetylase would enhance reprogramming and exogenous gene silencing in piPSCs. piPSCs induced by OSKM in combination with epigenetic factors, specifically Ten-Eleven-Translocation (Tet1 or Tet3) and lysine (K)-specific demethylase 3A (Kdm3a), expressed higher levels of Rex1 and other genes representing naïve state and exhibited more open chromatin status, in contrast to those of OSKM controls. Moreover, piPSCs induced by Tet1 combined with OSKM exhibited enhanced differentiation capacity. Conversion with histone deacetylase inhibitors, including NaB, TSA and VPA further increased expression of Rex1 and reduced expression of exogenous genes, generating high pluripotent piPSCs. Together, epigenetic modifiers can enhance generation of piPSCs and reduce their reliance on exogenous genes.

overall_design: RNA-seq for progenitor PEF, piPSCs P5 (Rex1+) and piPSCs P10 (Rex1-), in duplicate.

first: Kai

last: Liu

first: Lipu

last: Song

first: Xumin

last: Wang

first: Lin


title: Comparison 39ox and wt samples with or without fe-bHLH039 overexpression results in iron accumulation dependent on the FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR (FIT)

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

institute: IPS2_Institute of Plant Sciences Paris-Saclay

summary: au13-07_ox - comparison 39ox and wt samples with or without fe - Differential gene expression between 39Ox and WT at +Fe and -Fe - WT (Col-0) and 39Ox seeds were surface sterilized and grown directly on +Fe or -Fe Hoagland medium for 6 days. 60 whole seedlings were harvested in liquid nitrogen and grinded to a fine powder. Total RNA was extracted with the Spectrum Plant total RNA kit (Sigma-Aldrich). 8 µg total RNA was sent to analysis. For validation of the results, RT-qPCR was performed using the same RNA samples.

overall_design: 6 dye-swaps - normal vs. transgenic comparison, treated vs. untreated comparison.

first: Petra

last: Bauer

first: Sandrine

last: Balzergue

first: Marie

last: Martin-Magniette


title: ChIP-chip from four orangutan cells with CENP-A

city: Bologna

first: Stefania

last: Purgato

address: via Selmi 3

department: Pharmacy and Biotechnology

institute: University of Bologna

type: Genome binding/occupancy profiling by genome tiling array

summary: In the present study we analyzed centromeric localization on chromosome 12 in different orangutan and results showed that each individual exhibits a different arrangement of CENP-A binding domains.

sample_organism:
Pongo pygmaeus
Pongo abelii

platform_organism:
Pongo pygmaeus
Pongo abelii
Homo sapiens

overall_design: Comparison of four orangutan lymphoblastoid cell lines


title: Ets1 Regulates Genes Associated with Autoimmunity

status: Public on Dec 31 2016

city: Buffalo

first: Lee Ann

last: Sinha

state: NY

address: 701 Ellicott St

department: Biochemistry

institute: University at Buffalo


title: SK-NEP-1 treated with SKI-5C

city: suzhou

last: Pan

address: Jingde road 303

department: Department of Hematology and Oncology

institute: Children's Hospital of Soochow University

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

summary: Wilm’s tumor(WT) is the most common malignant renal tumor in children, representing approximately 6-14% of all childhood cancers and about 95% of all pediatric renal malignancies. SKI-5C is a newly developed Sphk1 inhibitor. This small molecular inhibitor was firstly reported at 2009 by Wang et al. This study investigated the antitumor activity of SKI-5C in SK-NEP-1 cells. SKI-5C inhibited cell proliferation of SK-NEP-1  cells in a dose-dependent manner. Annexin V, Tunel and Hochest 33342 staining analysis showed that SKI-5C-treated cells showed more apoptotic features compared with the control.

overall_design: SK-NEP-1 cells were treated with 2uM SKI-5C and control group cells were treated with the same volume of DMSO 24 hours later. Human LncRNA Array analysis was performed by KangChen Bio-tech, Shanghai P.R. China. Briefly, RNA purified from total RNA after removal of rRNA was amplified and transcribed into fluorescent cRNA and cDNA was labeled and hybridized to the Human LncRNA Array v3.0 (8660 K, Arraystar). 30,586 LncRNAs and 26,109coding transcripts which collected from the most authoritative databases such as RefSeq, UCSC Knowngenes, Ensembl and many related literatures can be detected by the microarray.

first: Tao

last: Fang

first: Pan

last: Jian


title: Analysis of gene expression profiles in wild-type vs Ets1-/- follicular B cells

summary: Ets1-/- mice have an increase in B cell differentiation to plasma cells and increased serum immunoglobulin levels. The genes in B cells that are transcriptionally regulated by Ets1 and help regulate B cell differentiation are largely unknown. Here, we identify Ets1-regulated target genes in B cells using ChIP-seq and RNA-seq analysis. We found that Ets1 targets  genes associated with immune response, mature B cell differentiation and regulation of B cell activation.

overall_design: Quiescent follicular B cells were sorted from the spleens of wild-type and Ets1-/- mice using the following markers B220+ CD23-high CD21-low CD80-negative IgA-negative IgE-negative IgG1-negative IgG2a-negative IgG2b-negative IgG3-negative. Total RNA was prepared from sorted cells and subjected to RNA-sequencing.

first: Prontip

last: Saelee

first: Lee

last: Garrett-Sinha


title: Analysis of Ets1 bound regions using ChIP-seq

overall_design: Splenic purified B cells from wild type mice were used for ChIP-seq


title: microRNA in chronic kidney disease (CKD)

city: Bellinzona

first: Luciano

last: Cascione

state: Ticino

address: Via Chiesa 5

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

overall_design: microRNA expression was assessed in normal tissue from patients developing CKD after radical nephrectomy for renal cancer (RCC), patients who did not develop CKD and healthy kidney donors

first: Nicola

last: Valeri


title: Deep Sequencing Leads to the Identification of Eukaryotic Translation Initiation Factor 5A as a Key Element in Rsv1-Mediated Lethal Systemic Hypersensitive Response to Soybean Mosaic Virus Infection in Soybean

city: London

first: Hui

last: Chen

state: Ontario

address: 1391 Sandford St.

institute: Agriculture and Agri-Food Canada

summary: We reported a genome-wide investigation to gain insight into the molecular signaling pathway involved in SMV G7 provoking Rsv1-mediated LSHR based on sRNA-seq, degradome-seq and transcriptome-seq analysis.

overall_design: mRNA, miRNAs and degradome profiles of Rsv1-genotype soybean (PI96983) after 14 days post-inoculation (dpi) by SMV-L (avirulent strain), SMV-G7 (virulent strain) and Mock (control) were generated by deep sequencing, pooled from three biological replicates (5 plants in each replicate) for each treatment, using Illumina Miseq.

first: Andrej

last: Arsovski

first: Kangfu

last: Yu

first: Aiming


title: ChIP-on-chip of BCL6 in follicular lymphoma

city: San Francisco

first: Huimin

last: Geng

address: 513 Parnassus Ave., MSB HSW 1201

department: Department of Laboratory Medicine

summary: Identification of BCL6 target genes in primary follicular lymphomas by ChIP-on-chip.

overall_design: ChIP-on-Chip was performed on four follicular lymphoma (FL) primary samples (WC15, WC16, WC17 and WC18) using an anti-BCL6 antibody.

first: Ester

last: Valls

first: Leandro

last: Cerchietti

first: Olivier

last: Elemento

first: Weimin

last: Ci

first: Ari

last: Melnick


title: Transcriptional signature in rat colonocytes in response to a high protein diet

status: Public on Dec 30 2016

city: Paris

first: Martin

last: BEAUMONT

address: 16  rue Claude Bernard

department: INRA AgroParisTech

institute: UMR914 PNCA

summary: High protein diet alter gut microbiota composition and activity. The objective of this study is to determine the consequences of a high protein diet for the colonic epithelium in rats.

overall_design: Wistar male  rats were fed a normal or a high protein diet  (NP and HP) during 15 days. At the end of the dietary intervention, colonocytes were isolated and RNA extracted.

last: Beaumont

first: Mireille

last: Andriamihaja

first: Lucie

last: Armand

first: Marta

last: Grauso

first: Florence

last: Jaffrezic

first: Denis

last: Laloë

first: Marco

last: Moroldo

first: Anne-Marie

last: Davila

first: Daniel

last: Tomé

first: François

last: Blachier

first: Annaïg

last: Lan


title: Genome-wide assessment of Nkx2.2 binding sites in MIN6 pancreatic beta cell line

status: Public on Dec 20 2016

first: Lori

last: Sussel

address: 1775 Aurora Ct.

institute: University of Colorado

summary: Through ChIP-Seq analysis we found Nkx2.2 to bind to important beta cell genes as well as to non beta endocrine ones.

overall_design: Examination of Nkx2.2 binding sites in MIN6 pancreatic beta cell line

first: Giselle

middle: D

last: Gutierrez

first: Aristotelis

last: Tsirigos

first: Stephen

last: Kelly


title: Gene expression in peripheral blood leukocytes in young endurance athletes

city: Shanghai

first: Dongmei

last: Liu

address: Henren Road, #188

department: Sports Rehabilitation

institute: Shanghai University of Sport

summary:
Exercise is beneficial to human’s health, and many of the effects are mediated by changes in immune function. However, the mechanisms underpinning the immune-regulatory effect of exercise remain unclear.
We used microarrays to assess the global gene expression in blood leukocytes in young endurance athletes and non-athlete controls, the differential gene expression between two groups was analzyed using bioinformatic methods and enriched biological processes and pathways were identified for up- and down-regulated genes in athletes.

overall_design: Twelve young endurance athletes and 11 age-, sex- and BMI-matched healthy non-athlete controls were included. A fasting blood sample was collected from each individual at rest. Blood leukocytes were extracted, and global gene expression profile was assessed using Affymetrix human gene 1.1 ST array. Group differences in the transcriptome were analyzed using powerful bioinformatic methods (Intensity-based Hierarchical Bayes method followed by a Logistic Regression-based gene set enrichment method).

first: Ru

last: Wang

first: Ana

middle: R

last: Grant

first: Jinming

last: Zhang

first: Gordon

last: Paul

first: Yuqin

last: Wei

first: Peijie

last: Chen


title: NKX2.2

city: Aurora

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Analysis of copy number variants on chromosome 21 in Down syndrome-associated congenital heart defects

status: Public on Jan 30 2017

city: Atlanta

first: Benjamin

last: Rambo-Martin

state: Georgia

address: 1600 Clifton Road

institute: Centers for Disease Contol and Prevention

summary: One in five people with Down syndrome (DS) are born with an atrioventricular septal defect (AVSD), an incidence 2,000 times higher than in the euploid population. The genetic loci that contribute to this risk are poorly understood. In this study, we tested two hypotheses: 1) individuals with DS carrying chromosome 21 copy number variants (CNVs) that interrupt exons may be protected from AVSD, because these CNVs return AVSD susceptibility loci back to disomy, and 2) individuals with DS carrying chromosome 21 genes spanned by microduplications are at greater risk for AVSD because these microduplications boost the dosage of AVSD susceptibility loci beyond a tolerable threshold. We tested 236 case individuals with DS+AVSD and 290 control individuals with DS and a normal heart using a custom microarray with dense probes tiled on chromosome 21 for array CGH. We found that neither an individual chromosome 21 CNV nor any individual gene intersected by a CNV was associated with AVSD in DS. Burden analyses revealed that African American controls had more bases covered by rare deletions than did African American cases. Inversely, we found that Caucasian cases had more genes intersected by rare duplications than did Caucasian controls. Pathway analyses indicated copy number perturbtations of genes involved in protein heterotrimerization and histone methylating proteins. Finally, we showed that previously DS+AVSD-associated common CNVs on chromosome 21 are likely false positives. This research adds to the swell of evidence indicating that DS-associated AVSD is similarly heterogeneous, as is AVSD in the euploid population.

overall_design: aCGH for CNV detection. A single reference individual with Down Syndrome was used for all samples, labeled with Cy3 (Channel 2).

first: Michael

last: Zwick


title: De novo transcriptome analysis of weed Apera spica-venti from seven tissues and growth stages

status: Public on Dec 15 2016

city: Slagelse

first: Khalid

last: Mahmood

address: Forsøgsvej 1

department: Agro-ecology

country: Denmark

institute: Aarhus University

summary: Loose silky bentgrass (Apera spica-venti) is an important weed in Europe. It can cause up to 30% yield loses. There is little molecular information available about this species. The lack of genetic information limits the biological understanding of this important noxious weed species such as growth, genetic variation, reproduction, biosynthesis of metabolites and metabolic mechanisms of herbicide resistance. This study produced a reference transcriptome for A. spica-venti from different tissues (leaf, root, stem) and various growth stages (seed at phenological stages 05, 07, 08, 09).

overall_design: Seeds from six herbicide susceptible populations of Apera spica-venti originating at six different locations in Denmark, were mixed together to create a meta-population encompassing a range of genetic variations possible within the species. Each of these six populations were previously tested between 2007 and 2010 with ALS and ACCase inhibitor herbicides and found to be susceptible (Mathiassen, pers. comm). Seeds were sown under greenhouse conditions on table with an automatic watering system. Leaf, stem, and root material from individual plant were harvested once the plants were at BBCH stage 34 to 36 (stem elongation). Tissues were cut in small pieces and immediately put in liquid nitrogen and then stored at -80°C. These tissues were kept separated by individual plant. Seeds from this meta-population were sown in 9 cm petri dishes with four filter papers and grown in a climate cabinet (Termaks Series KB8000L) at night/day temperatures of 10ºC /17ºC for 10h/14h, and imbibed with 5 mL of demineralized water. Germinated seeds were harvested at stage BBCH 05 (radicle emerges from seed), 07 (coleoptile emerges from caryopsis), 08 (coleoptile elongation), and 09 (Emergence: coleoptile breaks through soil surface). A total of 0.5 g of frozen tissue from leaf, stem, and root was grounded separately using a 2010 Geno/Grinder (SPEX Sample prep, Stanmore, UK) for 45 sec at 1,500 hertz and then soaked in liquid nitrogen. A total of 0.7 g of germinated seeds were grounded using the same method but for 2 cycles of 45 seconds at 1,500 hertz and were not soaked in liquid nitrogen. The RNA mini plant kit (Qiagen, Hilsen, Germany) was used for RNA extraction following the manufacturer protocol, three wash steps were performed. RNA quality was verified using a spectrophotometer (Nanodrop 3300, Wilmington, USA) and bioanalyzer (Agilent 2100, Santa Clara, USA). Samples that showed a RIN value of 6.0 and more were treated with DNAse 1 according to the protocol (Qiagen, Hilsen, Germany) and suspended in a final volume of 14 μL. RNA quality was verified again with spectrophotometer (NanoDrop-1000 v.3.1.0) and bioanalyzer using the RNA 6000 Plant Nano program (Agilent 2100). Samples with a RIN value higher than 6 were selected for cDNA library construction. The lower than recommended (>8) RIN value threshold selected here is because of difficulties in extracting high quality RNA from germinated seed samples. Nine libraries were created; seven for each of the individual tissues/growth stage samples, and two more libraries for leaf and root respectively to be sequenced by both 5’ and 3’ end for analysis of transcript start site because we believe they have the most important number of expressed genes of interest for future study. Samples of mRNA were selected and fragmentedand  transformed to 150-400 bp  short insert, strand specific cDNA libraries for sequencing on Illumina HiSeq 2500 with chemistry version 3 (Eurofins MGW, Germany)

first: Marielle

last: Babineau

first: Per

last: Kudsk

last: Kristensen