title: High throughput RNA sequencing of C. albicans colonizing the murine GI tract reveals a role for a secreted effecter in commensalism

status: Public on Dec 31 2018

city: San Francisco

first: Suzanne

last: Noble

address: 513 Parnassus Ave., Box 0414

institute: UCSF

summary: Candida albicans is a human gut commensal and an opportunistic pathogen. The ability to transition from yeasts to invasive hyphae is a central virulence attribute, but it is unclear how these two cell types function during commensal growth.  Using FISH to visualize C. albicans in a murine gut colonization model, we observed the co-occurrence of yeasts and hyphae throughout the gastrointestinal tract. Forward genetic analysis revealed that major transcriptional activators of yeast-to-hypha morphogenesis have unexpected activity as potent inhibitors of commensalism.  In vivo FISH, transcriptomic, and genetic analyses indicate that the morphogenesis program inhibits commensal fitness, not through control of cell shape as expected from in vitro studies, but by activating expression of a hypha-specific pro-inflammatory secreted protease and a hyphal cell surface adhesin. These results reveal a tradeoff between fungal programs supporting commensalism and virulence within the commensal niche in which selection against hypha-specific markers limits the disease-causing potential of this ubiquitous commensal-pathogen.

sample_organism:
Candida albicans
Mus musculus

platform_organism:
Candida albicans
Mus musculus

overall_design: WT (control) and ume6 (experimental) C. albicans strains were grown under 3 condtions (YPD 30C, 3 replicates; YPD+10% serum 37C, 3 replicates; and murine large intestine, 5 replicates) and then processed for gene expression analysis

first: Jessica

last: Witchley


title: Quantifying continuous cell-cycle phase using single-cell gene expression data

status: Public on Feb 12 2019

city: Chicago

first: John

middle: D

last: Blischak

state: IL

address: 920 E. 58th Street, CLSC 317

department: Human Genetics

country: USA

institute: University of Chicago

type: Expression profiling by high throughput sequencing

summary: The cell cycle is known to regulate cell proliferation and cell fate decisions, the underlying mechanism of which is well-studied and conserved across species and cell types. To date, the cell cycle is receiving a renewed importance due to the rapid advancement of single-cell genomics technology. Especially in the analysis of single-cell gene expression, the cell cycle plays a key role in understanding the expression variation across cell states and cell types. The current study was designed to develop effective tools for assessing and predicting the cell cycle in single-cell gene expression data analysis. We collected both Fluorescent Ubiquitination-based Cell Cycle Indicator (FUCCI) – for determining the cell cycle – and single-cell RNA-seq (scRNA-seq) data from each individual using STRT-seq on the Fluidigm C1 platform. The cells were collected from iPSCs derived from 6 genotyped Yoruba cell lines. The experimental design controlled for C1 processing batch effects, as well as individual and gender effects. Using these data, we developed a supervised approach for predicting the cyclical ordering of single cells in the cell cycle using single-cell gene expression data. We used the FUCCI fluorescent intensities to determine a cyclical ordering of the individual cells, and to assign cell time labels for individual cells representing each cell's position in one complete cell cycle. We estimated the cyclical trend of expression levels for each gene based on the FUCCI-derived cell times, and identified candidate sets of cyclical genes for model training. We trained our model in in 5-fold cross-validation and evaluate the trained model in held-out validation samples and external datasets. We compared the prediction results with existing approaches for estimating the cell cycle using single-cell gene expression data: including unsupervised approaches to construct the cyclical ordering of single cells and approaches to categorically assign the cell cycle to individual cells. These results provide a benchmark for assessing the cell cycle in scRNA-seq data analysis and insights into the effects of the cell cycle on gene expression variation in stem cells.

overall_design: We collected single-cell RNA sequencing (scRNA-seq) data using the Fluidigm C1 platform for induced pluripotent stem cell (iPSCs) lines from 6 previously genotyped Yoruba individuals from Ibadan, Nigeria (YRI). These iPSC lines were genetically engineered to express the FUCCI (Fluorescent ubiquitination cell cycle indicator) transgene, which uses fluorescently-tagged proteins to indicate the cell cycle status. We applied a balanced incomplete block design in which unique pairs of samples were distributed across 16 96-well plates of the C1 platform. This design allowed us to avoid confounding the individual and plate effects. Fluorescence images were captured for each plate with an automated single-cell observation system. Post imaging, scRNA-seq libraries were prepared with a STRT protocol modified for human iPSCs and sequenced on the HiSeq 2500. After quality control, the full data set included 888 single cells with fluorescence imaging and gene expression measurements for 11,040 genes.

first: Chiaowen

middle: J

last: Hsiao

first: Po-Yuan

last: Tung

first: Jonathan

middle: E

last: Burnett

first: Kushal

middle: K

last: Dey

first: Kenneth

last: Barr

first: Yoav

last: Gilad

first: Matthew

last: Stephens


title: Intestinal DNA methylome of preterm pigs

status: Public on Dec 18 2018

city: Shenzhen

first: Desheng

last: Gong

address: No.7 PengFei road

country: China

institute: Agricultural Genomes Institute at Shenzhen

type: Methylation profiling by high throughput sequencing

summary: DNA methylation plays important roles in normal development as well as sensing environmental exposures, thereby regulating transcription that is associated with cellular functions. Shortened gestational age and unexpected exposure to milk and microbes at the wrong time may affect intestinal development and health via DNA methylation. The present studies aimed to characterize the intestinal DNA methylomes of preterm neonates at birth and during postnatal development, in order to understand the cellular basis of the immature intestine and its interaction with early nutrition.

overall_design: In the present studies, preterm pigs were used as a model for preterm infants and the intestinal DNA methylome was analyzed by reduced representation bisulfite sequencing. In study 1, caesarean-delivered preterm or term pigs were euthanized shortly after birth or fed either total parenteral nutrition (TPN) or minimal enteral nutrition (MEN) using bovine colostrum (COL) for five days, followed by full enteral feeding with bovine milk until weeaing (26d). Intestinal DNA methylomes between preterm and term pigs at birth, on 5d and 26d were compared. In study 2, preterm pigs were fed MEN using either COL or infant formula (FOR) for five days, and intestinal DNA methylomes between 5d-old and newborn preterm pigs were compared.

first: Xiaoyu

last: Pan

first: Fei

last: Gao

first: Per

last: Sangild


title: Metabolic state determines drug response in liver cancer

status: Public on Nov 29 2018

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

country: Germany

institute: University Heidelberg

summary: Drug resistance is one of the most challenging problems in liver cancer research. The hepatocellular carcinoma cell line HLE is highly dependent on exogenous glutamine for proliferation. In this cell line, we have found that glutamine deprivation leads to proliferation arrest, phosphorylation of extracellular signal-regulated kinase (ERK), and metabolic alterations at gene, protein, metabolite levels. Interestingly, while HLE cells respond to kinase inhibitors in their unperturbed metabolic state, they display pro-tumourigenic phenotypes such as increased aerobic glycolysis and proliferation when treated with inhibitors of MAPK/ERK pathway in the impaired metabolic state induced by glutamine deprivation. Thus, the aim of this microarray analysis is to determine the genomic alterations that accompany glutamine deprivation and treatment with pERK inhibitor U0126. The anticipated alterations could shed light on novel molecular mechanisms underlying drug resistance, and may be useful for predicting therapeutic response in liver cancer.

overall_design: This microarray data includes the following conditions (and replicates): HLE cells cultured in complete media (n=2), HLE cells cultured in glutamine-free media (n=2), and HLE cells cultured in glutamine-free media containing 20 µM U0126 (n=2).

first: Zeribe

middle: C

last: Nwosu

first: Steven

last: Dooley

first: Weronika

last: Pioronska


title: Aging-associated patterns in the expression of human endogenous retroviruses

status: Public on Dec 07 2018

city: Tampere

first: Arttu

last: Autio

address: Arvo Ylpön katu 34

department: Faculty of Medicine and Life Sciences

country: Finland

institute: University of Tampere

summary: Human endogenous retroviruses (HERV) are relics of ancient retroviral infections in our genome. Most of them have lost their coding capacity, but proviral RNA or protein have been observed in several disease states (e.g. in inflammatory and autoimmune diseases and malignancies). However, their clinical significance as well as their mechanisms of action have still remained elusive. As human aging is associated with several biological characteristics of these diseases, we now analyzed the aging-associated expression of the individual proviruses of two HERV families, HERV-K (91 proviruses) and HERV-W (213 proviruses) using genome-wide RNA-sequencing (RNA-seq). RNA was purified from blood cells derived from healthy young individuals (n=7) and from nonagenarians (n=7). The data indicated that in the case of HERV-K (HML-2) 33 proviruses had a detectable expression but in only 3 of those the expression levels were significantly different between the young and old individuals. In the HERV-W family expression was observed in 45 loci and only in one case the young/old difference was significant. However, applying the hierarchical clustering on the HERV expression data resulted in the formation of two distinct clusters, one containing the young individuals and another the nonagenarians. This suggests, that even though the aging-associated differences in the expression levels of individual proviruses are minor, there seems to be some underlying aging-related pattern. These data indicate that aging does not have a strong effect on the expression of individual HERV proviruses, but instead several proviruses are affected moderately, leading to age-dependent expression profiles.

overall_design: Seven peripheral blood mononuclear cell (PBMC) samples from healthy nonagenarians, aged 94, all female. Seven PBMC samples from healthy young laboratory personnel, aged 26 to 32 median age 28, all female. RNA-sequencing of the samples was done. Expression of genes and human endogenous retroviruses (HERVs) was quantified.

first: Tapio

last: Nevalainen

first: Binisha

last: Hamal Mishra

first: Saara

last: Marttila

first: Marja

last: Jylhä

first: Mikko

last: Hurme


title: Azacitidine treated AML cells reveals highly variable cell surface proteome remodeling [Illumina]

status: Public on Nov 30 2018

city: La Jolla

first: Samuel

last: Danziger

state: CA

address: 10300 Campus Point Dr

institute: Celgene

type: Methylation profiling by genome tiling array

summary: Myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML) are diseases of abnormal hematopoietic differentiation with aberrant epigenetic alterations. Azacitidine (AZA) is a DNA methyltransferase inhibitor (DNMTi) widely used to treat MDS and AML, yet the impact of AZA on the cell surface proteome has not been defined. To identify potential therapeutic targets for use in combination with AZA in AML patients, we investigated the effects of AZA treatment on four AML cell lines representing different stages of differentiation. The effect of AZA treatment on these cell lines was characterized at three levels: the DNA methylome, the transcriptome, and the cell surface proteome. Untreated AML cell lines showed substantial overlap at all three omics level;  however, while AZA treatment globally reduced DNA methylation in all cell lines, changes in the transcriptome and surface proteome were subtle and differed among the cell lines. Transcriptome analysis identified five commonly upregulated coding genes upon AZA treatment in all four cell lines, TRPM4 being the only gene encoding a surface protein, and surface proteomics analysis found no commonly regulated proteins. Gene Set Enrichment Analysis (GSEA) of differentially-regulated RNA and surface proteins showed a decrease in metabolism pathways and an increase in immune defense response pathways. As such, AZA treatmentled to diverse effects at the individual gene and protein level but converged to common responses at the pathway level. Given the heterogeneous responses in the four cell lines,  the potential therapeutic strategies for AML in combinations with AZA are discussed.

overall_design: To study the effects of AZA treatment on the regulation of DNA methylation, each of the four cell lines was treated with AZA (0.5 μM) for 3 days, followed by a four-day drug holiday

first: Kevin

last: Leung

first: Aaron

last: Nguyen

first: Tao

last: Shi

first: Lin

last: Tang

first: Xiaochun

last: Ni

first: Laure

last: Escoubet

first: Kyle

last: MacBeth

first: Jorge

last: DiMartino

first: James

middle: A

last: Wells


title: Azacitidine treated AML cells reveals highly variable cell surface proteome remodeling

status: Public on Dec 01 2018

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

overall_design: Refer to individual Series


title: Spt6 is required for the fidelity of promoter selectivity

status: Public on Nov 01 2018

city: Boston

first: Fred

last: Winston

state: MA

address: 77 Avenue Louis Pasteur, Room 239

department: Genetics

institute: Harvard Medical School

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Spt6 is a conserved factor that controls transcription and chromatin structure across the genome. Although viewed as an elongation factor, spt6 mutations allow transcription from within coding regions, suggesting that Spt6 also controls initiation. To comprehensively characterize the requirement for Spt6 in transcription, we have used four approaches: TSS-seq and TFIIB ChIP-nexus to assay transcription initiation, NET-seq to assay elongating RNAPII, and MNase-seq to assay nucleosome occupancy and positioning. Our results demonstrate that Spt6 represses transcription initiation at thousands of intragenic promoters. We characterize these intragenic promoters, and find some features conserved with genic promoters and other features that are distinct. Finally, we show that Spt6 regulates transcription initiation at most genic promoters and propose a model of initiation site competition to account for this. Together, our results demonstrate that Spt6 controls the fidelity of transcription initiation throughout the genome and reveal the magnitude of the potential for expressing alternative genetic information via intragenic promoters.

overall_design: Transcription start site sequencing for two replicates each of wild-type and spt6-1004 S. cerevisiae strains after an 80 minute shift from 30ºC to 37ºC. ChIP-nexus of TFIIB in two replicates each of wild-type and spt6-1004 strains after an 80 minute shift from 30ºC to 37ºC. Native elongating transcript sequencing of a wild-type strain after an 80 minute shift from 30ºC to 37ºC (two replicates), and spt6-1004 strains grown at 30ºC or shifted to 37ºC for 80 minutes (two replicates each). Two replicates of ChIP-nexus of Spt6 in a wild-type strain grown at 30ºC. Two replicates of ChIP-nexus of Rpb1 in a wild-type strain grown at 30ºC. MNase-sequencing of wild-type (one experiment) and spt6-1004 strains (two replicates) shifted from 30ºC to 37ºC for 80 minutes.

first: Stephen

middle: M

last: Doris

last: Chuang

first: Olga

last: Viktorovskaya

first: Magdalena

last: Murawska

first: Dan

last: Spatt

first: L

middle: S

last: Churchman


title: Azacitidine treated AML cells reveals highly variable cell surface proteome remodeling [Affymetrix]

last: Danziger


title: Mushroom Body Ethanol RNA-seq

status: Public on Oct 25 2018

city: Providence

first: Emily

last: Petruccelli

state: Rhode Island

address: 185 Meeting Street

department: Neuroscience

institute: Brown University

summary: Lasting 24hr transcriptomic response of adult Drosophila mushroom body nuclei following odors only (odors) or odors+ethanol (trained) treatment.

overall_design: Adult male flies were sacrificed 24 hr after repeated treatments odors only (odors) or odors+ethanol (trained), and RNA was extracted from INTACT isolated mushroom body nuclei.

first: Karla

middle: R

last: Kaun


title: Array-based genome-wide transcriptome analysis of Minimally invasive follicular thyroid carcinomas

status: Public on Oct 01 2018

city: Sakai

first: OSAMU

last: ISHIBASHI

address: 1-1 Gakuen-cho, Naka-ku

department: Grad Sch Life & Environmental Sciences

country: Japan

institute: Osaka Prefecture University

summary: Minimally invasive follicular thyroid carcinoma (MI-FTC) is characterized by limited capsular and/or vascular invasion with good long-term outcomes. However, some cases of MI-FTC show a poor prognosis because of severe distant metastasis. Nonetheless, no method has been established for predicting the prognosis of MI-FTC. This study was conducted to identify novel prognostic factors for metastatic MI-FTC by use of the formalin-fixed paraffin-embedded (FFPE) specimens of this carcinoma.

overall_design: The tumorous and non-tumorous regions of FFPE thyroid specimens from 3 MI-FTC patients.

first: Osamu

last: Ishibashi

first: Tomoo

last: Jikuzono

first: Mitsuyoshi

last: Hirokawa

first: Iwao

last: Sugitani


title: Transcriptomic and genomic profiling of early-stage ovarian carcinomas associated with histotype and overall survival [RNA-Seq]

status: Public on Oct 04 2018

city: Gothenburg

first: Hanna

last: Engqvist

address: Medicinaregatan 1G

country: Sweden

institute: University of Gothenburg

summary: Ovarian cancer is the most lethal gynecological malignancy in the western world. Despite recent efforts to characterize ovarian cancer using molecular profiling, few targeted treatment options are currently available. Here, we examined genetic variants, fusion transcripts, SNP genotyping, and gene expression patterns for early-stage (I, II) ovarian carcinomas (n=96) in relation to clinicopathological characteristics and clinical outcome, thereby identifying novel genetic features of ovarian carcinomas. Furthermore, mutation frequencies of specific genetic variants and/or their gene expression patterns were associated with histotype and overall survival, e.g. SLC28A2 (mucinous ovarian carcinoma histotype), ARCN1 (low expression in 0-2 year survival group), and tumor suppressor MTUS1 (mutation status and overall survival). The long non-coding RNA MALAT1 was identified as a highly promiscuous fusion transcript in ovarian carcinoma. Moreover, gene expression deregulation for 23 genes was associated with tumor aggressiveness. Taken together, the novel biomarkers identified here may improve ovarian carcinoma subclassification and patient stratification according to histotype and overall survival.

overall_design: Whole-transcriptome RNA sequencing (RNA-seq) was performed for 96 early-stage primary invasive ovarian carcinomas.

first: Toshima

middle: Z

last: Parris

first: Elisabeth

last: Werner Rönnerman

first: Elin

last: Söderberg

first: Jana

last: Biermann

first: Claudia

last: Mateoiu

first: Karin

last: Sundfeldt

first: Anikó

last: Kovács

first: Per

last: Karlsson

first: Khalil

last: Helou


title: Chicken IRF7 knockout by CRISPR-Cas9 in DF-1 and in vitro H6N2 infection followed by RNA-seq

city: Davis

first: Huaijun

last: Zhou

address: Meyer 3307, One shields Ave.

institute: UC Davis

summary: To elucidate the functional role of chicken IRF7 against avian influenza virus (AIV) infection, we generated inducible IRF7 knockout DF-1 cell lines and performed in vitro infection using low pathogenic AIVs (LPAIVs) followed by RNA-seq.

overall_design: Transcriptiome analysis of low pathogenic influenza virus (H6N2) infected chicken IRF7 knockout DF-1 cell lines and control cell line at different timeponts (0, 2, 6, 12hpi)

first: Tae

last: Kim

first: Colin

last: Kern


title: Expression data of endothelium and hematopoietic cluster cells in the wild type and Steel mutant E11.5 AGM and vitelline and umbilical arteries

status: Public on Aug 30 2018

city: Oxford

first: Marella

last: de Bruijn

address: MRC MHU, WIMM, John Radcliffe Hospital

department: Radcliffe Department of Medicine

country: United Kingdom

institute: University of Oxford

summary: Kit ligand (Kitl, aka SCF) is a pivotal cytokine in fetal liver and bone marrow hematopoiesis. Its role in pre-liver embryonic hematopoiesis, however, is less well understood. We investigated the hematopoietic phenotype of Steel (Sl/Sl) mutant embryos, which lack Kitl, and found that the normal development of the HSC lineage in the aorta-gonad-mesonephros (AGM) region is negatively affected. We isolated endothelium and hematopoietic cluster cells from wild type and Sl/Sl AGM and vitelline and umbilical arteries for expression analysis by RNA-seq to investigate molecular changes in the developing HSC lineage and endothelial cells in the aortic HSC niche.

overall_design: AGM and vitelline and umbilical arteries were dissected from E11.5 wild type and Sl/Sl mouse embryos, pooled according to genotype, and sorted into Ter119- VE-Cadherin+ c-Kit- CD41- CD45- endothelial cells and Ter119- VE-Cadherin+ c-Kit+ hematopoietic cluster cells by flow cytometry. Two biological replicates per cell type passed all quality controls and were used for analysis. Each replicate contained 100 sorted cells. Each replicate was paired end sequenced across 3 lanes, creating 6 fastq files per sample replicate. cDNA synthesis and library preparation were performed by the Single Cell core facility at the MRC Weatherall Institute of Molecular Medicine (Oxford, UK).

first: Emanuele

last: Azzoni

first: Joe

last: Harman


title: Whole-transcriptome response of the cyanobacterium Synechocystis to hexan-1-ol

status: Public on Aug 11 2018

city: Moscow

first: Kirill

middle: S.

last: Mironov

address: Botanicheskaya str., 35

department: Molecular Biosystems

country: Russia

institute: K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Science

summary: We report the whole-transcriptome analysis of cyanobacterium Synechocystis culture response to the hexan-1-ol, 20 mM, 30-min treatment.

overall_design: 3 control and 3 treated samples

first: Dmitry

last: Los


title: Deregulated Expression of Mammalian lncRNA through Loss of SPT6 Induces R-Loop Formation, Replication Stress, and Cellular Senescence

status: Public on Nov 21 2018

city: Leicester

first: Michael

last: Tellier

state: Select State

address: Lancaster Road

department: Department of Molecular and Cell Biology

institute: University of Leicester

summary: RNA polymerase II (Pol II) generates interspersed protein-coding and long noncoding (lnc) transcripts across the mammalian genome. We recently established that lncRNAs are transcribed by different Pol II CTD isoforms correlating with reduced RNA processing efficiency and increased RNA turnover. How protein-coding and lncRNA transcription units are distinguished during gene expression remains unclear. We now show that H3K36me3 chromatin is a predominant epigenetic mark for active protein-coding but not lncRNA genes. Surprisingly depletion of the Pol II associated transcription elongation factor SPT6, causes redistribution of H3K36me3 histone marks to lncRNA genes which correlates with increased lncRNA transcription. SPT6 knockdown also reduces recruitment of Integrator complex to chromatin resulting in a transcription termination defect for lncRNA genes. Notably these extended lncRNAs are both chromatin-restricted and form increased levels of RNA:DNA hybrid (R-loops) with associated DNA damage. This results in a cellular senescence phenotype and underlies the importance of restricting lncRNA expression.

overall_design: After Spt6 knockdown, we performed in HeLa cells mNET-seq (total pol II, Thr4P), chromatin RNA-seq, nucleoplasmic RNA-seq, nuclear poly(A)+ RNA-seq, cytoplasmic RNA-seq, 3'seq sequencing, mNucD-seq (H3, H3K4me1, H3K4me3, H3K27me3, H3K36me3), ChIP-seq (INTS3, gamma H2AX) and DRIP-seq (R-loops RNA-sequencing)

first: Takayuki

last: Nojima

first: Jonathan

last: Foxwell

last: Rebeiro de Almeida

first: Sue

last: Tan-Wong

first: Somdhutta

last: Dhir

first: Ashish

first: Shona

last: Murphy

first: Nicholas

last: Proudfoot


title: Mapping of regions that are systematically under-replicated in metaphase and telophase, S. cerevisiae (2017-10-06)

status: Public on Jul 18 2018

city: Barcelona

first: Alsu

last: Missarova

address: Dr. Aiguader, 88

department: CEXS

country: Spain

institute: UPF

type: Genome variation profiling by high throughput sequencing

summary: We establish that subtelomeric regions together with some other functional elements like transposons are consistently under-replicated in metaphase and with lower extent in late anaphase, suggesting and ongoing DNA replication between metaphase and telophase.

overall_design: S. Cereivisiae mutants were arrested in either metaphase and G1-phase (6 replicates, by using a strain with methionine sensitive promoter in front of CDC20) or late anaphase and G1-phase (6 replicates, by using a strain with thermosensitive allele of DBF2

last: Maier


title: Mapping of regions that are systematically under-replicated in metaphase and establishing the role of CDK-inhibition in accomplishing DNA-replication in these regions, S. cerevisiae (2017-09-15)

summary: We establish that subtelomeric regions together with some other functional elements like transposons are consistently under-replicated in metaphase. Inhibition of CDK activity, in fact, results in accomplishing of DNA replication in those regions.

overall_design: To answer the question, we sequenced samples arrest in G1-phase and M-phase (by using a strain with methionine-sensitiver promoter, placed in front of CDC20). Additionally, we sequenced samples arrested in M-phase with additional inhibition of CDK activity

first: Tsvetomira

last: Ivanova


title: Mapping of regions that are systematically under-replicated during cell cycle stages


title: Mapping of regions that are systematically under-replicated in metaphase, S. cerevisiae (2017-03-23)

summary: We establish that subtelomeric regions together with some other functional elements like transposons are consistently under-replicated in metaphase.

overall_design: To answer the question, we sequenced samples arrest in G1-phase and M-phase (by using a strain with methionine-sensitive promoter, placed in front of CDC20). We compared Copy number of samples, arrested in different stages and analyzed regions where CN-r


title: Reconstruction of a Global Transcriptional Regulatory Network for Control of Lipid Metabolism in Yeast by Using Chromatin Immunoprecipitation with Lambda Exonuclease Digestion

status: Public on Jul 05 2018

city: Mölndal

first: David

last: Bergenholm

state: SWEDEN

address: Axgatan 139

institute: Chalmers tekniska högskola

summary: We performed whole genome analysis of the DNA binding of five Saccharomyces cerevisiae transcription factors involved in lipid biosynthesis, Ino2, Ino4, Hap1, Oaf1 and Pip2, in response to four different environmental conditions. Using chromatin immunoprecipitation with lambda exonuclease digestion (ChIP-exo) we discovered a large number of so-far unidentified targets with nucleotide resolution. Based on the newly identified targets we document expanded functions for all five transcription factors, e.g. glutamate biosynthesis as a target of Oaf1 and Pip2. Moreover, condition-dependent binding of transcription factors in response to cell metabolic state, e.g. differential binding of Ino2 between fermentative and respiratory metabolic conditions was clearly suggested. Using our data we build a comprehensive transcriptional regulatory network for lipid metabolism in yeast.

overall_design: The binding sites of Ino2, Ino4, Hap1, Oaf1 and Pip2 when cells were grown in Glucose-limited, Nitrogen-limited, Ethanol-limited or Oxygen/Glucose-limited chemostat cultivations were measured in biological duplicates

first: Guodong

last: Liu

first: Petter

last: Holland

first: Jens

last: Nielsen


title: RNA-seq of eight lymphoblastoid cell lines after AHR ligand treatments

status: Public on Jul 06 2018

city: Darlinghurst

first: Drew

last: Neavin

state: New South Wales

address: 384 Victoria St

department: Cellular Science

country: Australia

institute: Garvan Institute of Medical Research

summary: RNA-seq was done on eight different lymphoblastoid cell lines for vehicle control, 3-MC agonist treatment and GNF-351 antagonist treatment for AHR to look at AHR regulated genes with different genetic backgrounds.  We identified 69 genes that were highly differentially expressed after 3-MC or GNF-351 antagonist treatment with variation in the degree fo differential expression between the eight cell lines.

overall_design: Eight lymphoblastoid cells lines were treated in duplicate with vehicle control, 3-MC or GNF-351 for 24 hours before RNA collection.  Libraries were prepared on the TruSeq RNA Library Prep Kit v2 and paired end sequencing was carried out on Illumina HiSeq 4000

first: Richard

last: Weinshlboum

first: Liewei

last: Wang


title: Role of AHR in lymphoblastoid cell lines


title: A compendium of long non-coding RNAs transcriptional fingerprint in multiple myeloma

status: Public on Jun 05 2018

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

type: Non-coding RNA profiling by high throughput sequencing

summary: Multiple myeloma (MM) is a malignant proliferation of bone marrow plasma cells (PCs) characterized by highly heterogeneous genetic background and clinical course, and whose pathogenesis remains largely unknown. Long ncRNAs (lncRNAs) are a large class of non-protein-coding RNA, involved in many physiological cellular and genomic processes as well as in carcinogenesis, cancer metastasis and invasion. Although still in its infancy, the knowledge of the role of lncRNAs in MM is progressively expanding. Besides studies on selected candidates, lncRNAs expression at genome-wide transcriptome level is confined to microarray technologies, thus investigating a limited collection of transcripts.  Herein, we assessed the lncRNAs expression profiling by RNA-sequencing in a cohort of 30 MM patients, aimed at defining a comprehensive catalogue of lncRNAs specifically associated with the main MM molecular subgroups and genetic alterations. We identified 391 deregulated lncRNAs, 67% of which were also detectable and validated by whole-transcript microarrays. In addition, we identified a list of lncRNAs, with potential relevance in MM, co-expressed and in close proximity to genes that might undergo a cis-regulatory relationship.

overall_design: Total RNA samples from highly purified plasma cells of 30 MM cases at onset

first: Domenica

last: Ronchetti

first: Alessandro

last: Pietrelli

first: Katia

last: Todoerti

first: Martina

last: Manzoni

first: Elisa

last: Taiana

first: Antonino

last: Neri


title: Expression profile of mRNAs in PBMCs infected with CSF vaccine virus and Monocyte derived macrophages infected with virulent CSF virus of crossbred and indigenous pigs

status: Public on May 10 2018

city: Bareilly

first: AMIT

last: KUMAR

state: Uttar Pradesh

address: Izatnagar

department: Animal Genetics

country: India

institute: Indian Veterinary Research Institute

summary: Using high-throughput technology, we aim to identify the expression of mRNAs  for understanding the comparative pathogenesis of CSF in PBMCs and Macrophages of indigenous verses crossbred pigs.

overall_design: PBMCs were collected after 7 and 21 days post vaccination of  CSF vaccine virus and 60 hours post infection with virulant CSF virus in MDMs of crossbred and indigenous pigs to identify the global gene expression

first: Vaishali

last: Sah

first: Amit

last: Kumar

first: P

last: Dhar

first: V

last: Upmanyu

first: A

last: Tiwari

first: Sajad

last: Wani

last: Sahu

first: Ajay

first: S

last: Badasara

first: Aruna

last: Pandey

first: B

middle: P

last: Mishra

first: R

last: Singh

last: Gandham


title: Expression profile of miRNAs in PBMCs infected with CSF vaccine virus in six crossbred pigs

status: Public on May 14 2018

summary: Using high-throughput technology, we aim to identify the expression of miRNAs  for understanding the pathogenesis of CSF vaccine virus.

overall_design: PBMCs were collected on date of vaccination, 7th days and 21st days post vaccination. The miRNA expression were compared at 7dpv and 21 dpv as compared to control (PBMCs of prior to vaccination I.e. 0dpv)

first: Amitother

first: Lother

last: Sailo

first: Vaishaliother

first: Rajniother

last: Chaudhary

first: Arunaother

first: Raviother


title: miRNA microarray of rTDSCs under mechanical treatment or not

status: Public on May 24 2018

city: Shanghai

first: Yiyun

last: Geng

address: 320 Yue Yang Rd, Xuhui District

institute: Chinese Academy of Sciences

summary: Tendinopathy is a common disease in individuals whose tendons suffer from repetitive strains, such as athletes. The lack of knowledge regarding the pathological mechanisms causes inadequate prevention methods and low cure rate of this disease. Repetitive strain injury is thought to be the source of tendinopathy; therefore, we investigate the effect of mechanical loading on tendon and seek the ways to prevent and treat tendinopathy better. In our study, we found that the expression of a mechanosensitive miRNA, miR-337-3p, decreased in tendon-derived stem cells (TDSCs) under uniaxial cyclical mechanical loading with 10% elongation. In addition, miR-337-3p was negatively related to chondro-osteogenic differentiation of TDSCs, in which lower expression was found in human calcified tendons and rat tendinopathy samples.

overall_design: 3 samples of rTDSCs untreated as control, and 3 samples of rTDSCs under mechanical loading for 7days of 10% elongation,0.5Hz, 8h per day as treatment group

first: Xiaoling

last: Zhang


title: HIV-1 Tat  and Methamphetamine interaction in the mouse brain

status: Public on Mar 17 2018

city: San Diego

first: Maria

middle: Cecilia

last: Marcondes

address: 3525 John Hopkins Ct. #200

institute: San Diego Biomedical Research Institute

summary: Our goal was to examine whether the HIV Tat peptide, which is usually secreted from infected cells and has the potential to act in other cell types, alters gene expression in the Central Nervous System, and whether a drug abuse co-morbidity, in the case Methamphetamine, can play a role in further modifying gene expression. In order to address the effects of HIV Tat and Methamphetamine, alone and combined, we used an in vivo mouse model that has been described to mimic several aspects of neuroHIV, including changes in inflammatory markers, and decreased expression of dopamine receptors. These animals are transgenic mice, which upon treatment with with doxycycline for 10 days, express  TAT protein under the control of the glial fibrilary associated protein (GFAP) promoter in the brain. They were treated with Meth and Saline for identification of gene expression changes that result from Tat or Methamphetamine alone, or from their interaction. There was an overall suppression of gene expression by Methamphetamine, in Tat- mice. The expression of Tat caused most Meth-induced changes to remain at control levels.

overall_design:
A total of 20 male mice, 6 weeks old, 10 containing the GFAP promoter-controlled Tet-binding protein (TAT−) and 10 containing both the GFAP promoter-controlled Tet-binding protein and the TRE promoter-TAT protein transgene (TAT+) were tested. Inducible Tat transgenic mouse colonies with a C57BL/6J background are obtained by generation of two separate transgenic lines Teton-GFAP mice and TRE-Tat86 mice, and then cross-breeding of these two transgenic mouse lines, as previously described (Kim et al., 2003). The mice were housed in groups of 2–4 in a humidity- and temperature-controlled animal facility on a 12 h/12 h reverse light/dark cycle (lights off at 7:00 AM) with ad libitum access to food and water. All mice were treated with a doxycycline regimen (doxycycline hyclate; Sigma) of 100 mg/kg, intraperitoneally, once a day for 7 days. This regimen is based on the previously demonstrated efficacy of Tat induction at this dose of doxycycline (Carey et al., 2012; Paris et al., 2014a). Only mice containing both the GFAP promotor-controlled Tet-binding protein and the TRE promoter-TAT protein transgene (TAT+) generate TAT protein after doxycycline administration. Control TAT- animals had the GFAP promoter-controlled Tet-binding protein, but did not have TRE promoter-TAT protein transgene.  All mice (TAT+ and TAT-) were administered doxycycline injections in the evening (17:00 h), beginning the day before the first injection of Methamphetamine or Saline. The Methamphetamine  administration procedure followed a sensitization paradigm, and consisted of  seven consecutive days of intraperitoneal injection with either saline (0.9%) or 2 mg/kg methamphetamine (methamphetamine hydrochloride; Sigma, St. Louis, MO, USA). The animals were anesthesized and perfused with ice cold PBS 24 hrs after the last injection, and the brains were snap frozen for the determination of changes in the gene expression.
The animals were divided in 4 groups: G1=Tat-Meth+, G2=Tat-Meth-, G3=Tat+Meth+, G4=Tat+Meth-, and 5 mice per group.

first: Svetlana

last: Semenova

first: James

last: Kesby

first: Nikki

last: Bortell

first: Liana

last: Basova


title: A multi-component view of the glioma transcriptome identifies unique immune infiltration patterns in primary glioblastomas and patients with inferior prognosis.

status: Public on Mar 01 2018

city: Oslo

first: Jeanmougin

last: Jeanmougin

address: Ullernchausséen 70

department: Molecular Oncology

country: Norway

institute: Norwegian Radium Hospital

summary: Patients diagnosed with glioblastomas continue to have a dismal prognosis, highlighting the need for a better characterization of these tumors in order to identify more efficient therapies. In this study, we generated genome-wide expression data from normal brain and glioma samples, representing major glioma subtypes, using exon-level microarrays (n=70). A multi-component approach was used to characterize molecular pathways and tumor infiltrate, with particular focus on the poor prognosis primary glioblastomas (pGBM). Two independent, publically available datasets were used for validation of survival data. Grade II glioma and secondary GBM were enriched in cytotoxic lymphocytes, while pGBM exhibited a heterogeneous cell-related immune infiltrate with high infiltration of monocytic cells. Infiltration by cells of monocytic origin predicted poorer prognosis, regardless of the tumor subtype. High TSPYL2 expression was found to be associated with a poor prognosis in pGBM and to correlate with genes involved in tumor invasion. The multi-component transcriptome phenotypes of pGBM introduced in this study add insights into the main pathways associated with aggressiveness, and identified infiltration by cells of monocytic origin as a universal prognostic marker for all glioma subtypes.

overall_design: The study included 67 glioma samples which were grouped according to the 2016 revision of the WHO classification of tumors of the central nervous system. The study comprised 36 pGBM, 5 sGBM, 18 AII, and 8 OII from glioma patients who underwent surgery at the Department of Neurosurgery (Oslo University Hospital) between June 2006 and April 2010. Patients were included following written informed consent. Permission to include deceased patients was obtained from The National Health Authorities. The study was approved by the Regional Ethics Committee (S-06046) as well as the Institutional Study Board. Histological diagnoses were reviewed by an expert neuropathologist. Four commercially available normal brain total RNA samples were also included (BioChain, B209031, pool of 5 male donors; B306103, one male donor; Clonetech Laboratories, 1004311A, one male donor; Ambion, First Choice Human Brain - 105P055201A, pool of 23 donors). Tumor tissue samples were collected on RNAlater (Qiagen) and total RNA was extracted using a standard TRIzol protocol. Quantity and quality of RNA was assessed by NanoDrop ND-1000 Spectrophotometer (Thermo Fisher Scientific) and Agilent BioAnalyzer 2100 (Agilent Technologies), respectively. All samples were analyzed for global gene expression using Affymetrix Human Exon 1.0. ST Array (Thermo Fisher Scientific). Total RNA (250 ng) was used as input and processed according to the manufacturer's instructions, using the Ambion WT Expression Kit protocol (Ambion), Affymetrix GeneChip WT terminal labeling, and Hybridization User Manual (Affymetrix). Pre-processing and statistical analyses were performed using R version 3.2.2. For each sample, a CEL file storing intensity measures was generated by the Affymetrix GeneChip Command Console software (V.1.0). These files were further processed by background correction, quantile normalization, and summarization at the gene level by the robust multi-array average (RMA) approach using package oligo (version 1.34.2).

first: Marine

first: Annette

middle: B

last: Håvik

first: Lina

last: Cekaite

first: Petter

last: Brandal

first: Anita

last: Sveen

first: Torstein

last: Meling

first: Trude

middle: H

last: Ågesen

first: David

last: Scheie

first: Sverre

last: Hein

first: Ragnhild

last: Lothe

first: Guro

last: Lind


title: Systematic mapping of cell state trajectories, cell lineage, and perturbations in the zebrafish embryo using single cell transcriptomics

status: Public on Apr 26 2018

first: Daniel

last: Wagner

address: 200 Longwood Ave, Harvard Medical School, Systems Biology, Warren Alpert 536

department: Systems Biology

summary: High-throughput mapping of cellular differentiation hierarchies from single-cell data promises to empower systematic interrogations of vertebrate development and disease.  Here, we applied single-cell RNA sequencing to >92,000 cells from zebrafish embryos during the first day of development. Using a graph-based approach, we mapped a cell state landscape that describes axis patterning, germ layer formation, and organogenesis.  We tested how clonally related cells traverse this landscape by developing a transposon-based barcoding approach (“TracerSeq”) for reconstructing single-cell lineage histories. Clonally related cells were often restricted by the state landscape, including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin-deficient embryos. We provide web-based resources for further analysis of the single-cell data.

overall_design: Single-cell mRNA sequencing of zebrafish embryonic cells. Samples1-7: Single cell libraries from untreated embryos (4-24 hours post-fertilization). Samples8-12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1-cell stage. Samples13-18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1-cell stage.

first: Caleb

last: Weinreb

first: Zach

last: Collins

first: Sean

middle: G

last: Megason

first: Allon

last: Klein


title: Gene expression signatures between lean and diabetes resistant B6 mice and obese and diabetes susceptible NZO mice.

status: Public on Feb 27 2018

city: Nuthetal

first: Pascal

last: Gottmann

address: Arthur-Scheunert-Allee 114-116

institute: Deutsches Institut für Ernährungsforschung

summary: Whole genome microarray expression was measured in metabolic active tissues (gonadal white adipose tissue, brown adipose tissue and skeletal muscle) of 6 week old mice to detect changes in gene expression related to early onset of diabetes and obesity.

overall_design: Male NZO and B6 mice were kept on a high fat diet (HFD) until week 6. Than samples of gonadal white adipose tissue (gWAT), brown adipose tissue (BAT), and skeletal muscle were aliquoted for RNA extraction

first: Nicole

last: Hallahan

first: Anne

last: Kamitz

last: Schürmann


title: The transcriptome profile of French SLAdd pigs fed a standard diet suggests the presence of NAFLD

city: Jouy-en-Josas

first: Marco

last: Moroldo

address: Domaine de Vilvert

country: France

institute: INRA

summary: Blood samples from 60-day old SLAdd and Large White animals fed a standard diet were extracted in order to characterize the health status of the SLdd individuals, which showed symptoms of a NAFLD-related disorder

overall_design: Large White animals are used as controls for the study of SLAdd animals. There are 10 biological replicates for the SLAdd breed and 11 biological replicates for the Large White breed

first: Jérôme

last: Lecardonnel

first: Peris

last: Munyaka

first: Claire

last: Rogel-Gaillard


title: Differentially expressed genes in isolated postnatal AP2e WT and null VNOs

status: Public on Feb 03 2018

city: Albany

first: Paolo

last: Forni

state: NY

address: 1400 Washington Avenue

department: Biology

institute: Unversity at Albany

summary:
Understanding the molecular mechanisms defining and maintaining the identity of a specific neuronal cell type is a central goal in neuroscience. The vomeronasal organ (VNO) of mice contains hundreds of distinct vomeronasal sensory neurons (VSNs). The VSNs are classified into two major cell types that are segregated in apical and basal regions of the VNO, express vomeronasal receptors of different superfamilies, and send axons to different portions of the accessory olfactory bulb. How apical or basal identity of VSNs is established and maintained is largely unknown. Here we attempt to assess the role of a single transcription factor, AP-2ε, in the VNO of mice.
We used microarrays to examine global effect of AP-2ε loss-of-function on gene expression in the vomeronasal organ.

overall_design: Direct comparison between WT and AP2e-null VNOs

first: Jennifer

last: Lin

first: Sridar

middle: V

last: Chittur


title: Differential miRNA expression profiles of colorectal DLD1 and HT29 cell lines grown under 3D cell culture conditions

status: Public on Mar 30 2018

city: Vilnius

first: Vaidotas

last: Stankevicius

state: Lithuania

address: Santariskiu 1

country: Lithuania

institute: National Cancer Institute

summary: In the present study we investigated the microenvironment-dependent changes of miRNA expression in colorectal carcinoma DLD1 and HT29 cell lines. Next-generation sequencing technology was employed for the analysis of miRNA expression levels in cells cultivated under 3D multicellular spheroid and 2D culture conditions. The results of our study support the previous observations regarding the role of the tumor microenvironment in the regulation of gene expression. Furthermore, the profile of differentially expressed miRNAs, determined in the present study, could be applied for a further development of diagnostic and therapeutic applications in CRC.

overall_design: miRNA expression profiles of colorectal adenocarcinoma cells (DLD1 and HT29), grown in two-dimensional monolayer forming culture conditions or in three-dimensional multicellular spheroid culture were examined using Illumina HiSeq 2500 miRNA sequecing by Illumina HiSeq 2500 system.

first: Linas

last: Kunigėnas

last: Stankevičius


title: AHR ChIP-seq in lymphoblastoid cell line

first: Drew

last: Neavin

summary: ChIP-seq was done on one lymphoblastoid cell lines for vehicle control, or 3-MC agonist treatment to identify AHR binding regions throughout the genome. We identified 17,688 common binding peaks between all ChIP treatments

overall_design: A lymphoblastoid cell line was treated in duplicate with vehicle control or 1uM 3-MC 24 hours before cells were collected for ChIP-seq.  Sequencing was carried out on Illumina HiSeq 4000

first: Richard

last: Weinshlboum

first: Jeong-Heon

last: Lee

first: Zhenqing

last: Ye

first: Liewei

last: Wang


title: Effects of fosfomycin on biofilm of a clinical Staphylococcus aureus isolated from osteoarticular infection by transcriptomal approach

status: Public on Jan 31 2018

city: Clermont Ferrand

first: Christiane

last: Forestier

address: 28 Place Henri Dunant

department: Université de Pharmacie

institute: Laboratoire Microorganismes Génome et Enironnement

summary: The aim of the present study was to investigate the mechanisms by which fosfomycin restrains biofilm formation and affects a 24h-old biofilm of S. aureus. RNA sequencing (RNA-Seq) technology was used to compare the transcriptomes of S. aureus biofilms formed or treated with sublethal concentrations of fosfomycin.

overall_design: Determination of the transcriptional profiling of S. aureus under 4 different experimental conditions. mRNA profiles were generated for bacteria under 4 hours-old biofilm formed with and without fosfomycin and 24 hours-old biofilm treated or not with fosfomycin  for 24h, each in three biological replicates, by deep sequencing using Illumina HiSeq

last: Marquès

first: Valérie

last: Collin

first: Christine

last: Franceschi

first: Sonia

last: Chatellier


title: Genome-wide analysis of histone modification alteration at enhancer regions during epstein-barr virus infection.

status: Public on Aug 21 2017

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

institute: Chiba University

summary: We analysed epigenetic alterations by EBV infection especially at enhancer regions, to elucidate their contribution to tumorigenesis. We performed ChIP-seq on H3K4me3, H3K4me1, H3K27ac, H3K27me3 and H3K9me3 using gastric epithelial cells with or without EBV infection. We showed that repressive marks were redistributed after EBV infection, resulting in aberrant enhancer activation and repression. Enhancer dysfunction leads to activation of pathway related to cancer hallmarks (e.g. resisting cell death, disrupting cellular energetics, activation invasion, evading growth suppressors, sustaining proliferative signaling, angiogenesis and tumor promoting inflammation) and inactivation of tumour suppressive pathway. Dysregulation of cancer-related genes during in vitro EBV infection were also observed in EBV+ gastric cancer patients. Our analysis showed that EBV-infection associated epigenetic alteration may contribute to tumorigenesis through enhancer activation and repression.

overall_design: Examination of open chromatin regions and 2 different histone modifications in EBV infected or uninfected gastric cancer cells.

first: Atsushi

last: Okabe

first: Sayaka

last: Funata

last: Kaneda


title: Expression analysis of MADM based glioma mouse model

status: Public on Jun 30 2017

city: Nagoya

first: Keisuke

last: Katsushima

address: 1 Kawasumi, Mizuho-cho, Mizuho-ku

department: Department of Epigenomics

institute: Nagoya City University Graduate School of Medical Sciences

summary: Mosaic Analysis with Double Markers (MADM) based glioma mouse model, which homozygously lacks Tp53 and Nf1, spontaneously developed gliomas at the post-natal 90-120 days. Tp53 and Nf1 are among the most frequently mutated genes in human glioma patients. Investigating the expression changes of genes induced by inactivation of Tp53 and Nf1 can be a clue to clarify the mechanism of gliomagenesis. We examined the expressions of glioma in MADM mouse at post-natal 150 days (n=3) and of normal brain in Tp53 and Nf1 wild type mouse at post-natal 150 days (n=2). We used SurePrint G3 Mouse GE 8×60K array slides (G4858A, Agilent Technologies).

overall_design: Microarray experiment was performed as single-color hybridization on SurePrint G3 Mouse GE 8 x 60K array.

first: Akira

last: Hatanaka

first: Keiko

last: Shinjo

first: Fumiharu

last: Ohka

first: Toshihiko

last: Wakabayashi

last: Natsume

first: Yutaka

last: Kondo


title: Transcriptome profiling of the testis developing and spermatogenesis of Mongolian horse using RNA-Seq

status: Public on Jul 21 2017

city: Huhhot

first: Bei

last: Li

address: Zhaowuda Rd.306

institute: Inner Mongolia Agriculture University

summary: Genes have been identifed in mammalian testes ，and were essential for development of testis and spermatogenesis.

overall_design: In order to study those physiological processes, the 3 immature and 3 mature testis of Mongolian horse were collected and 6 libraries were established, using RNA-Seq, the related genes of Mongolian horse development of testis and spermatogenesis were detected.

first: Xiaolong

last: He


title: Effects of an Anguillicola crassus infection on steady-state mRNA levels in gas gland tissue of the European eel

status: Public on Aug 04 2017

city: Innsbruck

first: Gabriel

last: Schneebauer

address: Technikerstrasse 25

country: Austria

institute: University of Innsbruck

summary: We investigated transcriptional changes caused by the nematode Anguillicola crassus within yellow and silver eels by comparing gas gland tissues of uninfected yellow with infected yellow eels, and uninfected silver with infected silver eels, respectively. In yellow eel gas gland, the infection caused a modification of steady state mRNA levels of 1675 genes, most of them being upregulated. Functional annotation analysis based on GO terms was used to categorize identified genes with regard to swimbladder metabolism or response to the infection. In yellow eels, the most prominent category was ‘immune response’, including various inflammatory components, complement proteins, and immunoglobulins. The elevated expression of several glucose and monocarboxylate transporters indicated an attempt to maintain the level of glucose metabolism, even in due to the infection thickened gas gland tissue. In silver eel gas gland tissue, on the contrary, the mRNA levels of only 291 genes were affected. The reaction of the immune system was much less pronounced compared to infected yellow eels, but in the category ‘extracellular matrix’, the mRNA levels of several mucin genes were strongly elevated, suggesting increased mucus production as a defense reaction against the parasite. In summary, we found a strong reaction to an Anguillicola crassus infection on steady state mRNA levels in gas gland tissue of yellow eels, whereas in silver eels the changes ware almost negligible.

overall_design: Using Illumina Sequencing to obtain RNA-Seq data and statistical Deseq analysis, the transcriptomes of European eel gas gland tissues of animals with different development stages and different infection states were compared.

first: Ron

last: Dirks

first: Bernd

last: Pelster


title: Ablation of the Mammalian Lectin Galectin-8 Induces Bone Defects in Mice

status: Public on Nov 08 2017

city: Rehovot

first: Yehiel

last: Zick

address: 234 Herzl st.

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

summary: Mice overexpressing galectin-8 (gal-8 Tg), a secreted mammalian lectin, exhibit enhanced bone turnover and reduced bone mass, similar to cases of post-menopausal osteoporosis. Gal-8 knockout (KO) mice have increased bone mass accrual at young age, but exhibit accelerated bone loss during adulthood. These phenotypes can be attributed to gal-8-mediated increase in RANKL expression that promotes osteoclastogenesis, combined with direct inhibition of osteoblasts differentiation, evident by reduced BMP signaling, SMAD phosphorylation, and reduced expression of osteoblasts differentiation markers OSX, OCN, RUNX2, DMP-1 and ALP. Gal-8 mRNA positively correlates with the mRNA levels of osteoclastogenic markers RANKL, TRAP and CTSK in human femurs. Collectively, these findings identify gal-8 as a new physiological player in the regulation of bone mass.

overall_design: To elucidate the effect of galectin-8 on bone remodeling related genes, we compared gene expression profiles in non-treaed and galectin-8 treated (50nM, 24hrs) primary osteoblasts (OBL). OBLs were purified from calvaria of newborn mice, Total RNA was isolated, reverse-transcribed, fragmented, labeled and hybridized to Affymetrix GeneST 2.0 array.

first: Yaron

last: Vinik


title: Histone modification (H3K4me3, H3K27ac, and H3K27me3) change during EBV infection in gastric epithelial cells

last: Fukuyo

summary: Aberrant DNA hypermethylation is a major epigenetic mechanism to inactivate tumor suppressor genes in cancer, and Epstein-Barr virus (EBV) positive gastric cancer is known as the most frequently hypermethylated tumor among whole human malignancies. We here performed comprehensive analysis of epigenomic alteration during EBV infection, by Infinium HumanMethylation 450K BeadChip for DNA methylation and ChIP-sequencing for histone modification alteration. While 7,727 genes showed increase of DNA methylation in a promoter region, roughly half of these were “DNA methylation-sensitive” genes including anti-oncogenic genes e.g. CDKN2A and CDH1, which acquired DNA methylation in the whole promoter regions, thus leading to gene repression. Another half were “DNA methylation-resistant” genes including DNA repair genes, where DNA methylation is acquired in the surrounding of promoter regions but unmethylated status is protected in the vicinity of transcription start site, with gene expression retained. Histone modification alteration also occurred dynamically during EBV infection, in coordinated manner with DNA methylation alteration. DNA methylation-sensitive genes significantly correlated with loss of H3K27me3 pre-marks or decrease of active histone marks e.g. H3K4me3 and H3K27ac, and apoptosis-related genes were significantly enriched in these epigenetically repressed genes. Gain of active histone marks significantly correlated with DNA methylation-resistant genes, and genes related to mitotic cell cycle and DNA repair were significantly enriched in these epigenetically activated genes. Orchestrated epigenetic alterations play an important role in gene regulation during EBV infection, and histone modification status in promoter regions significantly associated with acquisition of de novo DNA methylation or protection of unmethylated status at TSS.

overall_design: Examination of 3 different histone modifications in EBV infected or uninfected gastric cancer cells.

last: Okabe


title: Sex differences in microglial developmental gene expression programs

status: Public on Jun 19 2017

city: Philadelphia

first: mark

last: alter

state: PA

address: 125 S. 31st Street

department: Center for Neurobiology and Behvior

country: USA

institute: University of Pennsylvania

summary: During normal neurodevelopment, microglia perform a range of different functions that are crucial for the proper development, circuit integration, and function of neurons. These functions include certain types of synaptic pruning during critical stages of neurodevelopment (Schafer et al., 2012), and the production of cytokines and chemokines during normal physiological tasks, proteins which are important for homeostasis in addition to immune defense (Avital et al., 2003; Goshen et al., 2007). Microglia and the inflammatory cytokines they produce (e.g., in response to injury or infection) are also increasingly implicated in neural dysfunction during development and the risk of neuropsychiatric disorders.  Increasing evidence suggests many neurological disorders emerge because of disrupted neuronal developmental trajectory (Marin, 2016). Considering the critical role of microglia for integration of neurons into their proper circuitry as well in proper synapse formation, there is a pressing need to understand the mechanisms underlying normal and abnormal microglia development, their interactions with specific neuronal subsets, and to understand the utility of these same analyses for human tissue.  Moreover, as there are pronounced sex differences in the presentation of many neurological disorders, it is critical to understand these mechanisms in both males and females. Here we study developmental gene expression changes in male and female mice from E18 to P60. We isolated microglia from male and female hippocampi of mice from different developmental ages ranging from embryonic day 18 (E18) to postnatal day 60 (P60). Hippocampus was selected based on its importance to mental health, its marked vulnerability relative to other brain regions in response to diverse threats to homeostasis (epilepsy, stroke, and cardiac arrest (Fujioka et al., 2000; Petito, Feldmann, Pulsinelli, & Plum, 1987; Salmenpera, Kalviainen, Partanen, & Pitkanen, 1998; Sapolsky, Uno, Rebert, & Finch, 1990)), and due to evidence of morphological sex differences in microglial development in this region (Schwarz, Sholar, & Bilbo, 2012). It was found that developmental gene expression changes were more advanced in females at P60 and that treatment with LPS, a potent immune activator, could normalize developmental gene expression differences in males.

overall_design: developmental timecourse in males and females; LPS vs. Saline at P60 in males and females

first: Mark

last: Alter

first: Staci

last: Bilbo


title: Expression profiling of control vs. ta/tbx16 double knockdown zebrafish embryos at shield and 90% epiboly

status: Public on Jun 11 2017

city: Coventry

first: Andrew

middle: Christopher

last: Nelson

address: Gibbet Hill Campus

department: School of Life Sciences

institute: University of Warwick

summary: Identification of genes downstream of ta/tbx16 in zebrafish embryos, and identification of direct targets by reference to Ta and Tbx16 ChIP-seq data

overall_design: Triplicate control and ta/tbx16 double morpholino injection samples for each stage.  Total RNA prepared from ~200 embryos per sample.

first: Stephen

last: Cutty

first: Fiona

last: Wardle


title: Genome-wide profiling of Ta, Tbx16 and Mixl1 binding in early zebrafish embryos

summary: Identification of Ta and Tbx16 binding sites during gastrulation, and Mixl1 binding sites during endoderm specification

overall_design: Replicate ChIP samples for Ta, Tbx16 and Mixl1 with matched input samples - 6x ChIP samples (2 per factor); 3x input samples

middle: J


title: Microarray and ChIP-seq identification of Ta and Tbx16 target genes in zebrafish gastrulas and Mixl1 targets in blastulas

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

overall_design: Refer to individual Series


title: An integrative analysis of non-coding regulatory DNA variations associated with autism

status: Public on Apr 25 2017

city: Brisbane

first: Sarah

middle: Marguerite

last: Williams

state: QLD

address: QBI Building 79, University of Queensland, St Lucia

department: Queensland Brain Institute

institute: University of Queensland

summary: A number of genetic studies have identified rare protein-coding DNA variations associated with autism spectrum disorder (ASD), a neurodevelopmental disorder with significant genetic etiology and heterogeneity. In contrast, the contributions of functional, regulatory genetic variations that occur in the extensive non-protein-coding regions of the genome remain poorly understood. Here we developed a genome-wide analysis to identify rare single nucleotide variants (SNVs) that occur in non-coding regions and determined regulatory function and evolutionary conservation of these variants. Using publicly available datasets and computational predictions, we identified SNVs within putative regulatory regions in promoters, transcription factor binding sites, microRNA genes and their target sites. Overall, we found regulatory variants in the ASD cases were enriched in autism-risk genes and genes involved in fetal neurodevelopment. As with previously reported coding mutations, we found an enrichment of regulatory variants associated with dysregulation of neurodevelopmental and synaptic signaling pathways. Among these were rare inherited non-coding SNVs found in the mature sequence of a number of microRNAs predicted to affect the regulation of autism-risk genes. We show a paternally inherited miR-873-5p variant, with reduced NRXN2 binding affinity, overlays a maternally inherited NRXN1 putative loss-of-function coding variation to likely increase genetic liability in an idiopathic ASD case. Our analysis pipeline provides a new resource for identifying loss-of-function regulatory DNA variations that may contribute to the genetic etiology of complex disorders.

overall_design: This data is RNAseq of tagged-microRNA mRNA-pulldown assays for wild-type and mutant miR-873-5p. Four replicates each, with paired control (con) and pulldown (PD) samples for each replicate.

first: Joon-Yong

last: An

first: Janette

last: Edson

first: Michelle

last: Watts

last: Whitehouse

first: Colin

last: Jackson

last: Bellgrove

first: Alexandre

last: Cristino

first: Charles

last: Claudianos


title: The Rodent-Specific MicroRNA Cluster within the Sfmbt2 Gene is Imprinted and Essential for Placental Development [miRNA]

status: Public on Feb 01 2017

city: Tsukuba

first: Kimiko

last: Inoue

state: Ibaraki

address: 3-1-1 Koyadai

department: Bioresource Engineering Division

institute: BRC, RIKEN

summary: MicroRNAs (miRNAs) represent small noncoding RNAs that are involved in physiologic and developmental processes by negatively regulating expression of target genes. They exist as individual miRNA genes or as polycistronically transcribed gene clusters. The largest miRNA cluster in mice is located in intron 10 of the Sfmbt2 gene, and contains 72 miRNA precursor sequences within approximately 50 kb. Although this miRNA cluster emerged recently in the rodent genome, probably coincidentally with the acquisition of the imprinted control of Sfmbt2, very little is known about its functions. In this study, we generated mice lacking the entire Sfmbt2 miRNA cluster to elucidate its functions during development. Like the Sfmbt2 gene, the Sfmbt2 miRNAs were expressed in the placenta predominantly from the paternal allele. Loss of the paternal allele resulted in severely impaired development of the spongiotrophoblast layer, which usually comprises about half of the fetal placenta. This phenotype was associated with fetal developmental delay or lethality, leading to significant decreases in the number of fetuses and their weights at term. Microarray analysis identified that at least 30 miRNAs in the cluster were actively transcribed in wild-type placentas. Among the predicted targets of these miRNAs, 132 genes were upregulated in the miRNA-deleted placentas. Some of the genes most significantly upregulated, including Gkn2 and Runx1, are known to inhibit cell proliferation by inducing cell cycle arrest or apoptosis. Thus, the Sfmbt2 miRNAs play essential roles in promoting trophoblastic cell proliferation in the placenta, cooperating with the host gene under the same paternal expression control.

overall_design: MicroRNA (miRNA) from mouse placentas were measured by microarray analysis. To identify target genes of Sfmbt2 miRNA cluster, gene expressions of placentas derived from wildtype and Sfmbt2 miRNA-deleted mice were measured. All placentas were collected in embryonic day 11.5 fetuses and more than four replicates were performed.

first: Atsuo

last: Ogura


title: Expression data from primary breast tumors, M0 patients

status: Public on Jun 09 2017

city: Rotterdam

first: Marcel

last: Smid

address: Dr. Molewaterplein 50

department: Medical Oncology

country: Netherlands

institute: Erasmus MC

summary:
Expression data were used to predict  the activity status of diverse pathways, which were compared to Tamoxifen response
152 samples from 135 unique breast cancer patients were used to establish the activity of transcriptomic pathways.

overall_design: Comparison of response to Tamoxifen

first: John

last: Martens

first: Wim

last: Verhaegh

first: Anja

last: van de Stolpe

first: Anieta

last: Sieuwerts


title: The Rodent-Specific MicroRNA Cluster within the Sfmbt2 Gene is Imprinted and Essential for Placental Development [mRNA E8.5]

overall_design: MicroRNA (miRNA) from mouse placentas were measured by microarray analysis. To identify target genes of Sfmbt2 miRNA cluster, gene expressions of placentas derived from wildtype and Sfmbt2 miRNA-deleted mice were measured. All placentas were collected in embryonic day 8.5 and 11.5 fetuses and more than four replicates were performed.


title: Primary breast tumors


title: The Rodent-Specific MicroRNA Cluster within the Sfmbt2 Gene is Imprinted and Essential for Placental Development [mRNA E11.5]


title: DNA methylation heterogeneity defines a disease spectrum in Ewing sarcoma

status: Public on Jan 30 2017

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

summary: Developmental tumors in children and young adults carry few genetic alterations, yet they have diverse clinical presentation. Focusing on Ewing sarcoma, we sought to establish the prevalence and characteristics of epigenetic heterogeneity in genetically homogeneous cancers. We performed genome-scale DNA methylation sequencing for a large cohort of Ewing sarcoma tumors and analyzed epigenetic heterogeneity on three levels: between cancers, between tumors, and within tumors. We observed consistent DNA hypomethylation at enhancers regulated by the disease-defining EWS-FLI1 fusion protein, thus establishing epigenomic enhancer reprogramming as a ubiquitous and characteristic feature of Ewing sarcoma. DNA methylation differences between tumors identified a continuous disease spectrum underlying Ewing sarcoma, which reflected the strength of an EWS-FLI1 regulatory signature and a continuum between mesenchymal and stem cell signatures. There was substantial epigenetic heterogeneity within tumors, particularly in patients with metastatic disease. In summary, our study provides a comprehensive assessment of epigenetic heterogeneity in Ewing sarcoma and thereby highlights the importance of considering nongenetic aspects of tumor heterogeneity in the context of cancer biology and personalized medicine.

overall_design: DNA methylation sequencing for a cohort of 140 Ewing sarcoma tumor samples, 16 Ewing sarcoma cell lines, and 32 primary mesenchymal stem cell samples


title: Comparing gene expression timing and amplitude to delineate the unique pathways of brown and white rot wood-degrading fungi

status: Public on Jan 05 2018

city: saint paul

first: Jonathan

last: Schilling

state: minnesota

address: 2004 folwell ave

institute: University of Minnesota

summary: Wood-degrading fungi play a critical role in global carbon cycling, and their varied mechanisms for deconstruction offer pathways for industrial bioconversion. In this study, we used comparative genomics to isolate upregulation patterns among fungi with brown rot (carbohydrate-selective) or white rot (lignin-degrading) nutritional modes. Specifically, we used whole-transcriptome profiling to compare early, middle, and late decay stages on wood wafers, matching differentially-expressed gene (DEG) patterns with fungal growth and enzyme activities. This approach highlighted 34 genes uniquely upregulated in early brown rot stages, with notable candidates involved in generating reactive oxygen species (ROS) as a pretreatment mechanism during brown rot. This approach further isolated 18 genes in late brown rot stages that may be adapted to handle oxidatively-reacted lignocellulose components. By summing gene expression levels in functional classes, we also identified a broad and reliable distinction in glycoside hydrolase (GH) versus lignocellulose oxidative (LOX) transcript counts that may reflect the energy investment burden of lignin-degrading machinery among white rot fungi.

sample_organism:
Pleurotus ostreatus
Trametes versicolor
Rhodonia placenta
Gloeophyllum trabeum

overall_design: We sequenced mRNA from 36 samples, including two brown rot and two white rot fungi, to compare the gene regulations of these two typical wood decay strategies. Each specie was used to colonize wood wafer directionally, a space for time experimental design for study wood decay successions. Then, 3 wood sections on wood wafer were sampled for RNA extraction, representing early to late decay stages, with 3 bioreplicates for each wood section for each specie.

first: Jiwei

last: Zhang

first: Kevin

last: Silverstein

first: Melania

last: Figueroa


title: CDK7 inhibition suppresses Castration-Resistant Prostate Cancer through MED1 inactivation

status: Public on Aug 20 2019

city: PHILADELPHIA

first: Irfan

last: Asangani

address: 421 Curie Bld.

department: Cancer Biology

summary: We performed RNA-seq and ChIP-seq in three prostate cell lines (VCaP, LNCaP and DU145) to ascertain the role of the mediator complex MED1 in AR signaling. Upon androgen stimulation, MED1 undergoes phosphorylation by CDK7 and physically engages with AR at super-enhancer sites, which is essential for AR-mediated transcription. The CDK7 specific inhibitor THZ1 blunts AR-dependent neoplastic growth by preventing the co-recruitment of AR/MED1 in a genome-wide fashion, and reverts the enzalutamide resistance characterized by hyper-phosphorylated MED1. The effect of THZ1 phenocopies that for MED1 and CDK7 knockdown.

overall_design:
Genome wide gene expression levels  in three prostate cancer cell lines (VCaP, LNCaP and DU145) were determined using RNA-seq.  The RNA-seq experiments were performed under three treatment conditions: (i) Treatment for 6 hrs with VEH/DHT/DHT+THZ1 (VCaP and LNCaP), (ii) treatment for 24hrs with DMSO/THZ1 (VCaP, LNCaP and DU145), and  (iii) knockdown of MED1 and CDK7 in VCaP and LNCaP cell lines.  We also determined using ChIP-seq the genome-wide binding levels of AR, MED1, and H3K27ac, in VCaP and LNCaP cells for treatment condition (i).

Genome wide binding levels of AR and MED1  in VCaP prostate cancer cell lines were determined using ChIP-seq.  The ChIP-seq experiments were performed under three treatment conditions, namely VEH, DHT stimulation for 6hrs with or without treatment with 200 nM THZ1.

first: Ram

last: Natesan


title: The Rodent-Specific MicroRNA Cluster within the Sfmbt2 Gene Is Imprinted and Essential for Placental Development

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


title: Regulatory logic of the coupled diurnal and feeding cycles in the mouse liver

status: Public on Dec 31 2016

city: Lausanne

middle: Aryeh

last: Sobel

state: Vaud

address: EPFL SV IBI-SV UPNAE AAB 0 36 (Batiment AAB) Station 15

country: Switzerland

institute: EPFL

summary:
This study is a follow-up to GSE35790.

This SuperSeries is composed of the SubSeries listed below.


title: Regulatory logic of the coupled diurnal and feeding cycles in the mouse liver [DNase-seq, ChIP-seq]

summary: Understanding the kinetics of circadian transcriptional regulation has recently advanced thanks to genome-wide dynamic mapping of RNA Polymerase II, chromatin marks such as histone 3 modifications, and several core clock regulatory factors. To obtain deeper mechanistic insights into the determinant of phase-specific transcription, we here extend previous analyses of the CycliX Consortium by integrating new genome-wide datasets enabling systematic identification of active regulatory regions in the mouse liver. DNase I hypersensitive sites (DHS)-mapping within nuclear chromatin is a powerful method to identify active regulatory elements in the genome. Experiments were performed throughout the diurnal cycle to obtain a temporal map of active regulatory elements. In addition, we quantified H3K27ac, which mark active regulatory regions, throughout the diurnal cycle and RNA Polymerase II using chromatin immunoprecipitation data analysis. DHS were validated as likely regulatory elements by footprinting analyses and overlaps with published ChIP-seq datasets. Analysis of the regions displaying diurnal patterns revealed promoter, transcription start site (TSS)-proximal and TSS-distal elements potentially involved in the regulation of rhythmic gene transcription. Peak phases of DNase I accessibility and H3K27ac levels correlated well with RNA Polymerase II loadings, and regulatory elements oscillated with phases close to those of nearest TSS, which prompted us to use these signals to infer regulatory relationships. Comparisons with results in a Bmal1 -/- genotype (KO) revealed comparable levels of diurnal transcription oscillations likely driven by nutrient and food-entrained rhythms. Using linear modeling, we inferred activities of transcription factors around the clock in WT and KO datasets to reveal that in absence of a functional core circadian clock, FOX transcription factors and glucocorticoid receptor appear to be the main drivers of phase-specific expression. This raises the interesting question of whether light-driven circadian entrainment from the central pacemaker in the SCN acts to counter effect food-related signals.

overall_design:
ChIP-seq of PolII, ChIP-seq of H3K27ac and DNase1-seq in WT C57/B6 and Bmal1KO mouse liver in 12h light-12h dark conditions. Three mice samples pooled every four hours from ZT2 to ZT26. DNase-1 seq done only for ZT 6 in Bmal1KO mice.

The wild-type input samples for this study are included in GSE35790 (Samples GSM874971-GSM874977).

Contributor: CycliX Consortium

first: Irina

last: Krier

first: Teemu

last: Andersin

first: Sunil

last: Raghav

first: Donatella

last: Canella

first: Federica

last: Gilardi

first: Alexandra

last: Kalantzi

first: Guillaume

last: Rey

first: Matteo

last: Dal Peraro

first: Nouria

last: Hernandez

first: Ueli

last: Schibler

first: Bart

last: Deplancke

first: Felix

last: Naef


title: Ancestral (bi-)polarization control module in free-living and obligate intracellular bacteria

status: Public on Dec 23 2016

city: Geneva

first: Antonio

last: Frandi

address: rue michel servet 1

department: Microbiology and Molecular Medicine

institute: University of Geneva

summary: We report here the zitS DNA binding by ZitP and PopZ in Caulobacter crescentus. Also the parS site bound by ParB are showed. From chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of ParB, ZitP and PopZ DNA binding. We find that ZitP and PopZ binds DNA close to the parS site. This study provides evidence that PopZ and ZitP participates in DNA segregation in C. crescentus.

overall_design: DNA binding of ParB, ZitP and PopZ was analysed by chromatin immunoprecipitation-deep sequencing, and found to bind zitS site surrounding the parS site

first: Matthieu

last: Bergé

first: Sébastien

last: Campagne

first: Johann

last: Mignolet

first: Seamus

last: Holden

first: Laurence

last: Théraulaz

first: Suliana

last: Manley

first: Frédéric

middle: T

last: Allain

first: Patrick

last: Viollier


title: A novel GPR120-dependent pathway of control brown fat activation mediated by FGF21

status: Public on Dec 12 2016

city: Barcelona

first: Francesc

last: Villaroya

address: Avda Diagonal 643

department: Facultat de Biologia

institute: Universitat de Barcelona

summary: Brown adipose tissue (BAT) thermogenesis and the browning of white adipose tissue are important components of energy expenditure. An RNAseq-based analysis of the mouse BAT transcriptome led us to identify GPR120 as a gene induced by thermogenic activation. GPR120, a G protein-coupled receptor binding unsaturated long-chain fatty acids, is known to mediate some beneficial metabolic actions of polyunsaturated fatty acids. We show that pharmacological activation of GPR120 induces BAT activity and promotes the browning of white fat in mice, whereas GRP120-null mice show impaired browning in response to cold. n-3 polyunsaturated fatty acids induce brown and beige adipocyte differentiation and thermogenic activation, and these effects require GPR120. GPR120 activation induces the release of fibroblast growth factor-21 (FGF-21) by brown and beige adipocytes and increases blood FGF21 levels. The effects of GPR120 activation are impaired in FGF21-null mice and cells. Thus, the lipid sensor GPR120 constitutes a novel pathway of brown fat activation and involves FGF21.

overall_design: eight adult male C57BL6 mice were maintained at thermoneutral temperature (29C). After two weeks, a subset of four mice was placed at 4C environment temperature for 24h. RNAseq was performed on the BAT tissues of these 2 groups.

first: Tania

last: Quesada-López

first: Rubén

last: Cereijo

first: Jean-Valery

last: Turatsinze

first: Anna

last: Planavila

first: Montserrat

last: Cairó

first: Aleix

last: Gavaldà-Navarro

first: Marion

last: Peyrou

first: Ricardo

last: Moure

first: Marta

last: Giralt

first: Decio

last: Eizirik

last: Villarroya


title: Sex differences in tendon structure and function

status: Public on Aug 11 2016

city: Ann Arbor

first: Christopher

middle: Louis

last: Mendias

state: Michigan

address: 109 Zina Pitcher Place

department: Orthopaedic Surgery

institute: University of Michigan

summary: Tendons play a critical role in the transmission of forces between muscles and bones, and chronic tendon injuries and diseases are among the leading causes of musculoskeletal disability. For many types of tendinopathies, women have worse clinical outcomes than men. It is possible that sex-based differences in tendon morphology, composition and mechanical properties may explain the greater susceptibility of women to develop tendinopathies. Our objective was to evaluate the mechanical properties, biochemical composition, transcriptome, and cellular activity of plantarflexor tendons from four month old male and female C57Bl/6 mice using in vitro biomechanics, mass spectrometry-based proteomics, genome-wide expression profiling, and cell culture techniques. Differences between groups were tested using t-tests (α=0.05). While the Achilles tendons of male mice were approximately 6% larger than female mice (P<0.05), the cell density of female mice was around 19% larger than males (P<0.05). No significant differences in the length (P=0.34), peak force (P=0.86), peak stress (P=0.52) or energy loss during stretch (P=0.94) of plantaris tendons were observed. Mass spectrometry proteomics analysis revealed no significant difference between sexes in the abundance of major extracellular matrix (ECM) proteins like collagen types I (P=0.30) and III (P=0.68), but female mice had approximately two-fold elevations (P<0.05) in different minor ECM proteins such as fibronectin, periostin, and tenascin. Using microarray analysis, there was no significant differences (P>0.05) in the expression of most major and minor ECM genes, and in the expression of genes involved in tendon fibroblast specification or proliferation. Whole tendon qPCR analysis showed significant expression differences in elastin, scleraxis, and tenomodulin. Cell culture techniques to test the effects of sex-specific extracellular environment on cellular activity show significant differences in gene expression of type I and III collagen, Ki67, scleraxis, and tenomodulin. Histologic analysis demonstrated that males have larger tendon cross-sectional area and lower cell density when compared to females. However, there were no differences between the sexes in the mechanical properties of tendons or in the majority of primary structural extracellular matrix proteins, although elevations were observed in some minor ECM proteins. Microarray analysis also showed no significant sex-based differences in the expression of major genes associated with collagen composition, extracellular components and turnover, and fibroblast proliferation. Cell culture tests of non-autonomous cellular activity show no major signals for ECM synthesis nor fibroblast proliferation. Our results indicate that while male mice expectedly had larger tendons, male and female mice have very similar mechanical properties and biochemical composition, with small increases in minor ECM proteins and proteoglycans in female tendons. The role that these minor ECM proteins and proteoglycans play in tendon repair should be evaluated in future studies.

overall_design: No treatment administered, study done to evaluate normal expression profiles of male and female tenocytes. This analysis is based on a Mouse Gene ST 2.1 strip that was processed in the microarray facility in May 2015 using the wt-pico kit.

first: Dylan

middle: C

last: Sarver

first: Yalda

last: Ashrav-Kharaz

first: Kristoffer

last: Sugg

first: Jonathan

last: Gumucio

first: Eithne

last: Comerford

middle: L

first: Craig

last: Johnson


title: Critical modulation of hematopoietic lineage fate by the PAR/bZIP transcription factor Hepatic Leukemia Factor

status: Public on Jul 11 2016

city: Cambridge

first: Evangelia

last: Diamanti

address: Wellcome Trust / MRC Building, Hills Road

department: Haematology

institute: University of Cambridge

summary: Blood cell formation is a tightly regulated process initiated from a rare population of multipotent hematopoietic stem cells. Subsequent differentiation proceeds in a hierarchical manner with the generation of intermediate progenitor cells, in which alternative lineage potentials become gradually restricted. A deeper understanding of these events is crucial not only to understand normal blood cell formation, but also for leukemia, where a defining feature is inappropriate differentiation. Here, we identified Hepatic Leukemia Factor (Hlf) as being highly and selectively expressed in primitive multipotent hematopoietic stem and progenitors. We demonstrate that Hlf is a strong negative regulator of B-, NK- and T cell development and instructs multipotent progenitors to adopt a myeloid fate in a cell autonomous manner; phenotypes underwritten by the induction of myeloid affiliated transcriptional programs, the concomitant ablation of lymphoid gene programs and genome-wide binding spectra that involved active enhancers of myeloid-competent cells. Collectively, our studies establish Hlf as a key regulator of the earliest lineage-commitment events at the transition from multipotency to lineage-restricted progeny, with implications for both normal and malignant hematopoiesis.

overall_design: Identification of Hlf binding sites in Lin-Sca-1+c-Kit+ cells

first: Martin

last: Wahlestedt

first: Vasileios

last: Ladopoulos

first: Petter

last: Säwén

first: Mattias

last: Magnusson

first: Gudmundur

last: Norddahl

first: Manuel

middle: S

last: Castillo

first: Rebecca

last: Hannah

first: Berthold

last: Göttgens

first: David

last: Bryder


title: Next generation sequencing to elucidate the novel function of RORC (RORgamma) in breast cancer

status: Public on Dec 01 2016

city: St Lucia

first: Tae Gyu

last: Oh

address: 306 Carmody Rd

institute: Institute for Molecular Bioscience

summary: Exploring the novel role of RORC (RORgamma) in breast cancer, utilizing NEXTseq with genetic gain and loss of function and pharmacological treatment.

overall_design: For loss of function, control-siRNA or RORC-siRNA was transfected for 48h in three cell lines (MCF-7, T-47D and MDA-MB-231). For gain of function, CMV-empty or CMV-RORC was transfected for 48h in MDA-MB-231 cells. Furthermore, the selective RORC antagonist, SR2211 was utilized. MCF-7 cells were treated either DMSO or SR2211 (5uM) for 24h. Total RNA was extracted with the RNeasy kit. NEXTseq was performed for transcriptome analysis.

first: Tae

first: George

middle: E

last: Muscat


title: ASSISTED REPRODUCTIVE TECHNOLOGIES ALTER DNA METHYLATION PROFILES IN BLOODSPOTS OF NEWBORN INFANTS

status: Public on Aug 31 2016

city: New York

first: Molly

last: Estill

address: 1 Gustave L. Levy Place

department: Neuroscience

institute: Mount Sinai School of Medicine

summary: The Illumina Infinium HumanMethylation 450k Beadchip was employed to study the impact of in-vitro fertilization on DNA methylation in peripheral blood of infants.  Using a total of 137 Michigan newborns born through IVF using fresh embryo transfer, IVF using cryopreserved embryo transfer, Intrauterine Insemination, or unassisted conception, DNA from archived Guthrie cards was assayed for methylation profiles.

overall_design: A study in differential methylation, DNA from 137  archived bloodspots were bisulphite converted and assayed using the  Infinium HumanMethylation 450k Beadchip

first: Jay

last: Bolnick

first: Robert

middle: A

last: Waterland

first: Alan

first: Michael

last: Diamond

first: Stephen

last: Krawetz


title: Patients With Proneural Glioblastoma May Derive Overall Survival Benefit From the Addition of Bevacizumab to First-Line Radiotherapy and Temozolomide: Retrospective Analysis of the AVAglio Trial

status: Public on Jul 06 2016

city: South San Francisco

first: Richard

last: Bourgon

address: 1 DNA Way, MS 93

department: Bioinformatics & Computational Biology

institute: Genentech, Inc.

summary:
The AVAglio and RTOG-0825 randomized, placebo-controlled phase III trials in newly diagnosed glioblastoma reported prolonged progression-free survival (PFS), but not overall survival (OS), with the addition of bevacizumab to radiotherapy/temozolomide. To establish whether certain patient subgroups derived OS benefit from the addition of bevacizumab to first-line standard-of-care therapy, AVAglio patients were retrospectively evaluated for molecular subtype, and bevacizumab efficacy assessed for each patient subgroup.

A multivariate analysis accounting for prognostic covariates revealed that bevacizumab conferred a significant OS advantage versus placebo for patients with Proneural IDH1 wild-type tumors (17.1 v 12.8 months, respectively; hazard ratio, 0.43; 95% CI, 0.26 to 0.73; P = .002). This analysis also revealed an interaction between the Proneural subtype biomarker and treatment arm (P = .023). The group of patients with Mesenchymal and Proneural tumors derived a PFS benefit from bevacizumab, compared with placebo; however, this translated to an OS benefit in the Proneural subset only.

Retrospective analysis of AVAglio data suggests that patients with IDH1 wild-type Proneural glioblastoma may derive OS benefit from first-line bevacizumab treatment. The predictive value of the Proneural subtype observed in AVAglio should be validated in an independent dataset.

overall_design: A total of 349 (bevacizumab arm, n = 171; placebo arm, n = 178) pretreatment specimens from AVAglio patients (total n = 921) were available for biomarker analysis. Samples were profiled for gene expression and isocitrate dehydrogenase 1 (IDH1) mutation status and classified into previously identified molecular subtypes. PFS and OS were assessed within each subtype.

first: Thomas

last: Sandmann

first: Josep

last: Garcia

first: Congfen

last: Li

first: Timothy

last: Cloughesy

first: Olivier

last: Chinot

first: Wolfgang

last: Wick

first: Ryo

last: Nishikawa

first: Warren

last: Mason

first: Roger

last: Henriksson

first: Frank

last: Saran

first: Albert

last: Lai

first: Nicola

last: Moore

first: Samir

last: Kharbanda

first: Franklin

last: Peale

first: Priti

last: Hegde

first: Lauren

last: Abrey

first: Heidi

last: Phillips

first: Carlos

last: Bais


title: Laser-capture microscopy coupled with Smart-seq2 (LCM-seq) for robust and efficient transcriptomic profiling of mouse and human tissues

status: Public on Jul 05 2016

city: Stockholm

first: Eva

last: Hedlund

address: Svante Arrhenius v. 16C

department: Department of Biochemistry and Biophysics

institute: Stockholm University

summary: Generally, when LCM is used in diverse transcriptomic analyses, several hundred, if not thousands, of cells are needed to obtain high quality of RNA-seq data. As some cellular populations are very small and tissue often in scarcity, we aimed to carefully document the lowest number of cells needed to retrieve sequencable libraries. We started with capturing 120 cells and subsequently scaled down to 50 cells, 30 cells, 10 cells, 5 cells, 2 cells and finally 1 cell. By optimizing multiple steps in the procedure, including direct lysis of cells without performing RNA isolation, we developed LCM-seq that couples LCM with Smart-seq2 for robust and efficient polyA-based RNA sequencing. We applied LCM-seq to mouse and human neuron samples, and demonstrated that LCM-seq can allow us to acquire high quality RNA-seq data from mouse and human tissues to conduct various transcriptomic studies.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Developing new sequencing technology LCM-seq to efficiently sequence mouse and human tissues

first: Geng

last: Chen


title: Genome-wide analysis of long noncoding RNA expression profile in colorectal cancer

status: Public on Nov 26 2016

city: Changsha

first: Wu

last: Hao

state: Hunan

address: 138 Tongzipo Road

department: Department of General Surgery

country: China

institute: The Third Xiangya Hospital of Central South University

summary: Human colorectal cancer (CRC) is the third most common cancer in the world.Recent studies have shown that long non-coding (lncRNA) plays critical roles in a myriad of biological processes and human diseases,Since the roles of lncRNA in CRC remain largely unknown,they were investigated in the study.Our findings indicate that the expression profiles of lncRNAs has changed in CRC as compared with adjacent non-tumor samples, and may provide novel insight into the molecular mechanism underlying the disease and potential novel diagnostic or therapeutic targets for CRC.

overall_design: Microarray expression profiling of mRNAs and lncRNAs were conducted using RNA extracted from three colorectal cancer tumor samples and three matched adjacent non-tumor samples

first: Xiaorong

last: Li

first: Hao

last: Wu

first: Changwei

last: Lin

first: Jian

first: Chaoqun

last: Qin


title: Epigenomic Atlas of Early Human Craniofacial Development

status: Public on May 04 2017

city: Philadelphia

first: Justin

last: Cotney

address: 3501 Civic Center Blvd

department: Surgery

institute: Children's Hospital of Philadelphia

summary:
Chromatin State Profilining using multiple histone modifications in human craniofacial tissue spanning 4.5 post conception weeks to 10 pcw
The raw FASTQ sequence files are being deposited in dbGAP

overall_design: Parallel profiling of six distinct histone modifications via ChIP-Seq in craniofacial tissue samples from individual human embryos


title: PWC dataset for genome-wide association study of modifiers of risk of canine degenerative myelopathy in dogs homozygous for SOD1 mutation

status: Public on Jun 01 2016

first: Kerstin

last: Lindblad-Toh

address: 715 Main Street

department: Vertebrate Genome Biology

institute: Broad Institute

summary: Degenerative myelopathy (DM) is a canine disease very similar to amyotrophic lateral sclerosis (ALS) in humans. We previously showed that DM is a promising model for ALS, as genome-wide association identified a mutation in SOD1, a known ALS gene. In this study, we identify a modifier gene, SP110, which strongly affects overall disease risk and age-of-onset in Pembroke Welsh corgis at risk of DM. Dissecting the complex genetics of this disease in a model organism may lead to new insights about risk and progression in both canine and human patients.

overall_design: 15 DM-affected and 31 unaffected PWC homozygous for SOD1 mutation genotyped using the Illumina CanineHD array (~170,000 SNPs genomewide)

first: Emma

last: Ivansson

first: Katherine

last: Megquier


title: Expression data from mouse induced Erythroid Progenitor (iEP)-derived colonies, mouse bone marrow and fetal liver BFU-Es and mouse fibroblasts.

status: Public on Apr 22 2016

city: Lund

first: Shamit

last: Soneji

address: Solvegatan 19

institute: BMC

summary:
Forced expression of Gata1, Tal1, Lmo2 and c-Myc reprograms murine adult fibroblasts into erythroid progenitor cells. The resulting cells, called induced erythroid progenitors/precursors (iEPs), resemble bona fide erythroid cells in terms of morphology, colony forming capacity, and gene expression.
We used microarrays to characterize the reprogrammed cells (iEP_red and iEP_non-red) at the molecular level and compare their global gene expression profile with bona fide erythroid cells (FL and BM BFU-Es) and starting fibroblasts (Fibs).

overall_design: To obtain mRNA from pure cell populations, BFU-E colony-forming assays were performed on day 5-iEPs as well as on mouse E14.5 fetal liver cells and bone marrow cells. Eight days after, colonies were picked and processed for RNA extraction. Cultured fibroblasts were collected as controls.

first: Capellera-Garcia

last: Sandra

first: Soneji

last: Shamit


title: Global gene expression profiling of Jmjd6- and Jmjd4-depleted mouse NIH3T3 fibroblasts

status: Public on Jan 12 2016

city: Worcester

first: Yu-Jie

last: Hu

address: 55 Lake Avenue North

department: Cell & Developmental Biology

institute: UMass Medical School

summary: Emerging evidence suggests Jumonji domain-containing proteins are epigenetic regulators in diverse biological processes including cellular differentiation and proliferation. RNA interference-based analyses combined with gene expression profiling can effectively characterize the cellular functions of these enzymes. We found that the depletion of Jumonji domain-containing protein 6 (Jmjd6) and its paralog protein Jumonji domain-containing protein 4 (Jmjd4) individually by small hairpin RNAs (shRNAs) slowed cell proliferation of mouse NIH3T3 fibroblasts. We subsequently performed gene expression profiling on both Jmjd6- and Jmjd4-depleted mouse NIH3T3 fibroblasts using the Affymetrix GeneChip Mouse Exon 1.0 ST Array.

overall_design: We anaylzed control shRNA-treated cells, Jmjd6- and Jmjd4- depleted cells using Affymetrix Mouse Exon 1.0 ST platform. Two biological replicates were performed (total 6 samples). Array data was processed by Affymetrix Expression Console.

first: Anthony

middle: N

last: Imbalzano