title: CXCL8 and CXCR1 Remodel the Vascular Niche to Promote Hematopoietic Stem and Progenitor Cell Colonization and Engraftment [huvec CXCL8 vs control]

status: Public on Mar 24 2017

first: Leonard

last: Zon

state: MA

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

summary: The microenvironment is an important regulator of hematopoietic stem and progenitor cell (HSPC) biology.  Interactions between the niche and stem cells have been difficult to track, but recent advances marking fluorescent HSPCs have allowed exquisite visualization in the caudal hematopoietic tissue (CHT) of the developing zebrafish.  Sinusoidal endothelial cells interact closely with HSPCs as they colonize this niche.  Here we show that the chemokine cxcl8 and its receptor, cxcr1, are abundantly expressed by zebrafish endothelial cells and we identify cxcl8/cxcr1 signaling as a positive regulator of HSPC colonization using genetic gain- and loss-of-function techniques.  Single-cell tracking experiments demonstrated that this effect is due to an increase in HSPC “cuddling” by endothelial cells, thereby increasing CHT residency time and allowing more HSPC cell divisions to occur.  Enhanced cxcl8/cxcr1 signaling was associated with an increase in the volume of the CHT and induction of cxcl12a expression, favoring HSPC colonization.  Finally, using parabiotic zebrafish, we show that cxcr1 acts stem cell non-autonomously to improve the efficiency of donor HSPC engraftment.  This work identifies a mechanism by which the hematopoietic niche remodels to promote HSPC engraftment and suggests that cxcl8/cxcr1 signaling is a potential therapeutic target in patients undergoing hematopoietic stem cell transplantation.

overall_design: Primary human endothelial cells were serum starved for 12 hours followed by treatment with recombinant human CXCL8 or vehicle control for 6 hours.  Total RNA was collected from biological duplicates and RNA-seq libraries were prepared.

first: Bradley

middle: W

last: Blaser

first: Song

last: Yang


title: Comparison of gene expression in control bam-Gal4 and control undriven tbrd-2RNAi Drosophila testes with tbrd-2 knockdown testes

status: Public on Mar 23 2017

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

country: Germany

institute: Justus-Liebig-University Giessen

summary: Gene expression is tightly linked to histone acetylation on lysine residues that can be recognized by bromodomains. The testis-specific bromodomain protein tBRD-2 is essential for male fertility, interacts with tBRD-1 and might act as a co-factor of testis-specifc TAFs. Here, we perform microarray analyses and demonstrate that tBRD-2 selectively controls gene expression in male germ cells.

overall_design: Testes were dissected from 0-2 day old Drosophila males. The control samples were bam-Gal4 and undriven tbrd-2 RNAi. In addition testes from tbrd-2 knockdown males were used.

first: Christina

last: Rathke


title: CXCL8 and CXCR1 Remodel the Vascular Niche to Promote Hematopoietic Stem and Progenitor Cell Colonization and Engraftment [wt vs kdrl:cxcr1]

city: Boston

country: USA

type: Expression profiling by high throughput sequencing

overall_design: Kdrl:mcherry and kdrl:mcherry;kdrl:cxcr1 zebrafish were dissociated and endothelial cells purified by FACS.  RNA-seq libraries were prepared from endothelial cells purified from two independent clutches of fish (four libraries total).


title: An H5N1 virus-encoded atypical microRNA is a major contributor to cytokine storm and mortality

city: Nanjing

first: Zhen

last: Zhou

state: Jiangsu

address: 22th,Hankou Road

department: School of Lifesciences

country: China

institute: Nanjing University

type: Non-coding RNA profiling by high throughput sequencing

summary: An H5N1 virus-encoded microRNA directly targets mammalian poly(rC) binding protein 2 and is a major contributor to H5N1-associated ‘cytokine storm’ and mortality.

overall_design: Small RNA profiles of A549 cells infected with H5N1 influenza A virus infected were generated by deep sequencing, using Illumina Genome Analyzer.

first: Xihan

last: Li

first: Chen-Yu

last: Zhang


title: Transcriptome analysis of Streptococcus gallolyticus subsp. gallolyticus in interaction with THP-1 macrophages

status: Public on Mar 22 2017

city: Bad Oeynhausen

first: Imke

last: Grimm

address: Georgstraße 11

department: Institut für Laboratoriums- und Transfusionsmedizin

institute: Herz- und Diabeteszentrum NRW; Universitätsklinikum der Ruhr-Universität Bochum

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

overall_design: Refer to individual Series


title: Interaction between mitoNEET and NAF-1 in cancer cells

status: Public on Mar 25 2017

city: Denton

first: Rajeev

middle: K.

last: Azad

state: Texas

address: 1155 Union Circle #305220

institute: University of North Texas

summary: The NEET proteins mitoNEET (mNT) and nutrient-deprivation autophagy factor-1 (NAF-1) are required for cancer cell proliferation and resistance to oxidative stress. MitoNEET and NAF-1 are also implicated in a number of other human pathologies including diabetes, neurodegeneration and heart disease, as well as in development, differentiation and aging. Previous studies suggested that mNT and NAF-1 could function in the same pathway in cancer cells, preventing the over-accumulation of iron and reactive oxygen species (ROS) in mitochondria. Nevertheless, it is unknown whether these two proteins interact in cells, and how they mediate their function. Here we demonstrate, using yeast two-hybrid, in vivo bimolecular fluorescence complementation (BiFC), direct coupling analysis (DCA), RNA- sequencing, ROS and iron imaging, and single and double shRNA lines with suppressed  mNT, NAF-1 and mNT/NAF-1 expression, that mNT and NAF-1 interact in cancer cells and function in the same cellular pathway. We further show using an in vitro cluster transfer assay that mNT can transfer its clusters to NAF-1. Our study suggests that mNT and NAF-1 could function as part of an iron-sulfur (2Fe-2S) cluster relay to maintain the levels of iron and Fe-S clusters under control in the mitochondria of cancer cells, thereby preventing the activation of apoptosis and/or autophagy and thus promoting rapid cellular proliferation.

overall_design: Examination of the effect of suppression of mNT in the breast cancer cell line MCF-7. Two sample types were analyzed, MCF-7 suppressed for mNT and MCF-7 Empty vector control, three replicates for each.

first: Ola

last: Karmi

first: Sarah

middle: H

last: Holt

first: Yang-Sung

last: Sohn

first: Luhua

last: Song

first: Sagi

last: Tamir

first: Yuting

last: Luo

first: Ammar

last: Adenwalla

first: Patricia

middle: A

last: Jennings

first: José

middle: N

last: Onuchic

middle: K

first: Faruck

last: Morcos

first: Rachel

last: Nechushtai

first: Ron

last: Mittler


title: Transcriptome-wide analysis of alternative routes for RNA substrates into the exosome complex

status: Public on Mar 20 2017

city: Edinburgh

first: Clementine

last: Delan-Forino

address: Michael Swann Building 5.1, King's Buildings, Mayfield Road

country: United Kingdom

institute: University of Edinburgh - WTCCB

summary: The RNA exosome complex functions in both the accurate processing and rapid degradation of many different classes of RNA.  Functional and structural analyses indicate that RNA can either be threaded through the central channel of the exosome or more directly access the active sites of the ribonucleases Rrp44 and Rrp6, but it was unclear how many substrates follow each pathway in vivo. To address this we used UV crosslinking in growing cells to identify transcriptome-wide interactions of RNAs with the major nuclear exosome-cofactor Mtr4 and with individual exosome subunits  (Rrp6, Csl4, Rrp41 and Rrp44) along the threaded RNA path. We performed comparative analyses on exosome complexes lacking the exonucleolytic activity of Rrp44, either carrying a mutation in the Rrp44 S1 RNA-binding domain, predicted to disfavor direct access to the Rrp44 exonuclease active site, or with multiple mutations in Rrp41, reported to block RNA passage through the central channel.   Our analysis identified targets using preferentially channel-threading pathway such as mRNAs, 5S rRNA or scR1. Our results suggest as well that aborted tRNAs transcripts, released during transcription, would be rapidly degraded using this route. Alternatively, pre-tRNAs appears to access Rrp44 directly. Both routes seems to be involved for degradation or maturation of RNAPI transcripts.  The Rrp41 mutations were found to block substrate passage to Rrp44 only for cytoplasmic mRNAs, apparently confirming the prediction of widening of the lumen in the nuclear, Rrp6-associated complex.

overall_design: 13 samples were analysed from strains carrying HTP tagged protein. Duplicate CRAC experiments were carried out for each protein

first: Claudia

last: Schneider

first: David

last: Tollervey


title: CXCL8 and CXCR1 Remodel the Vascular Niche to Promote Hematopoietic Stem and Progenitor Cell Colonization and Engraftment

first: Leonard

last: Zon

sample_organism:
Danio rerio
Homo sapiens

platform_organism:
Danio rerio
Homo sapiens


title: Transcriptome analysis of Streptococcus gallolyticus subsp. gallolyticus in interaction with THP-1 macrophages [UCN 34 5h]

first: Imke

last: Grimm

summary: Background: Streptococcus gallolyticus subsp. gallolyticus (S. gallolyticus) is a pathogen of infective endocarditis. It was observed previously that this bacterium survives longer in macrophages than other species and the phagocytic uptake by and survival in THP-1 macrophages is strain-dependent.   Methods: The phagocytosis assay was performed with THP-1 macrophages. S. gallolyticus specific whole genome microarrays were used for transcriptome analysis.   Results: Better survival in macrophages was observed for UCN34, BAA-2069 and ATCC43143 than for DSM16831 and LMG17956. S. gallolyticus strains show high resistance to tested bactericidal agents (acid, lysozyme and hydrogen peroxide). S. gallolyticus stimulates significant lower cytokine gene expression and causes less lysis of macrophages compared to the control strain S. aureus. S. gallolyticus reacts to oxidative burst with a higher gene expression of NADH oxidase initially at the early phase. Expression of genes involved in D-alanylation of teichoic acid, carbohydrate metabolism and transport systems were upregulated thereafter.   Conclusion: S. gallolyticus is very resistant to bactericidal agents normally causing degradation of bacteria in phagolysosomes. Additionally, the D-alanylation of teichoic acid is an important factor for survival.

overall_design:
Analysis of two S. gallolyticus subsp. gallolyticus strains (BAA-2069 and UCN 34) at three different time points (-60min; 0h and 5h) of phagocytosis. For each time point and strain three biological replicates were taken and normalized on the -60min-timepoint.

This series contains 3 re-analyzed samples from GSE96861 (GSM2545273, GSM2545275, and GSM2545277).

first: Tanja

last: Vollmer

first: Jens

last: Dreier


title: Comprehensive evaluation of genome-wide 5-hydroxymethylcytosine profiling approaches in human DNA [MeDIP-seq]

status: Public on Mar 17 2017

city: Sydney

first: Ksenia

last: Skvortsova

state: NSW

address: 384 Victoria St, Darlinghurst

department: Genomics and Epigenetics

country: Australia

institute: Garvan Institute

type: Methylation profiling by high throughput sequencing

summary: The gold standard bisulphite conversion technologies to study DNA methylation do not distinguish between 5mC and 5hmC, however new approaches to map 5hmC genome-wide have advanced rapidly, although it is unclear how the different methods compare in accurately calling 5hmC. In this study, we provide a comparative analysis on brain DNA using three 5hmC genome-wide approaches; namely whole-genome bisulphite/oxidative-bisulphite sequencing (WG Bis/OxBis-seq), Infinium HumanMethylation450 BeadChip arrays coupled with oxidative bisulphite (HM450K Bis/OxBis) and antibody-based immunoprecipitation and sequencing of hydroxymethylated DNA (hMeDIP-seq). We also compare the performance of these approaches in adult brain DNA, with a known high abundance of 5hmC, and cancer cell line LNCaP DNA, with cell lines known to have low levels of 5hmC.

overall_design: For WG Bis/OxBis-seq, 200ng of DNA was treated in separate aliquots with CEGX bisulphite (Bis) and oxidative bisulphite (OxBis) reagents followed by library preparation and paired-end 150bp sequencing on Illumina HiSeqX platform using the HiSeq X™ Ten Reagent Kit v2. For HM450K Bis/OxBis, DNA was treated in separate aliqots with CEGX bisulphite (Bis) and oxidative bisulphite (OxBis) reagents with two replicas being performed for each Bis and OxBis workflow. For hMeDIP-seq, DNA was sonicated to the size range of 300-500bp. Prior to hMeDIP procedure, Illumina adaptors were ligated (5x 1ug) of fragmented DNA according to TruSeq LT DNA sample preparation kit (Illumina) followed by DNA denaturation and immunoprecipitation overnight with 5hmC polyclonal antibody (Active Motif cat no 55010).

first: Elena

last: Zotenko

first: Phuc-Loi

last: Luu

first: Cathryn

middle: M

last: Gould

first: Shalima

middle: S

last: Nair

first: Susan

middle: J

last: Clark

first: Clare

last: Stirzaker


title: Comprehensive evaluation of genome-wide 5-hydroxymethylcytosine profiling approaches in human DNA [BiSulfite-seq]


title: Comparison miRNA expression between atherosclerotic and non-atherosclerotic ischemic stroke patients

status: Public on Mar 16 2017

city: Daejeon

first: Jei

last: Kim

address: 282 Moonhwa-ro, Joong-gu

country: South Korea

institute: Chungnam National University Hospital

summary: The difference of circulating miRNA expressions by the presence of atherosclerosis in intra- and extra-cranial vessels were evaluated using serum of ischemic stroke patients.

overall_design: Serum from atherosclerotic (n=7) and non-atherosclerotic (n=8) patients were collected and miRNAs were extracted for miRNA microarray.

first: Jeeyeon


title: Tissue-Specific Transcriptomics Reveals Role of the Unfolded Protein Response in Maintaining Fertility upon Heat Stress in Arabidopsis - ChIP-Seq

status: Public on Mar 15 2017

city: Shanghai

first: Hongxing

last: Yang

address: 3888 Chenhua Rd, Songjiang District

institute: Shanghai Chenshan Botanical Garden

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Elevated temperature occurring at reproductive stage has great impact on gametophyte development and therefore ultimate fruit or seed set in plants, the underlying molecular mechanisms are less understood. We investigated the effect of elevated temperature stress on reproductive development in Arabidopsis with tissue-specific transcriptome profiling and observed distinct response patterns between vegetative and reproductive tissues. Heat stress exposure affected reproductive developmental programs including early phases of anther/ovule development and meiosis process, and genes participating in the unfolded protein response (UPR) were enriched among the heat up-regulated reproductive tissue-specific genes. We found that the bzip28bzip60 double mutant defective in UPR were sensitive to elevated temperature stress in terms of reduced silique length and fertility comparing to the wild-type plants. Comparison of heat responsiveness between the wild-type and bzip28zip60 plants identified 521 genes that were regulated by bZIP28 and bZIP60 upon heat stress at reproductive stage, most of which were non-canonical UPR genes. Further ChIP-Seq data revealed 133 direct targets of bZIP28 in Arabidopsis seedlings subjected to heat stress, of which 39 target genes were up-regulated by heat stress at reproductive stage. Our results provide novel insights into heat responsiveness in reproductive tissues and demonstrate the protective roles of UPR for maintaining fertility upon heat stress in plants.

overall_design: For ChIP-Seq assay, 13-day-old seedlings of 35S::MYC-bZIP28 plants were subjected to heat stress (42 0C for 1 hour) in triplicate, while the control was taken at 22 ℃. The CHIP assay was performed with procedure described before (Song et al., 2015). Protein A agarose beads (Millipore) with MYC antibody (Sigma) were used to precipitate the DNA. ChIP-DNA and input-DNA libraries were constructed and sequenced with Illumina HiSeq3000.

first: Jian-Xiang

last: Liu

first: Shuang-Shuang

last: Zhang

first: Fang

last: Chang

first: Hong

last: Ma


title: Tissue-Specific Transcriptomics Reveals Role of the Unfolded Protein Response in Maintaining Fertility upon Heat Stress in Arabidopsis

overall_design: Flowering plants were treated at 37 0C for 3 hours, while the controls were taken at 22 0C, after which the early flower (EL), late flower (LF), and rosette leaf (RL) were collected in triplicate. cDNA library was constructed from the extracted total RNA and sequenced with Illumina HiSeq3000.


title: Two microRNA Signatures for Malignancy and Immune Infiltration Predict Overall Survival in Advanced Epithelial Ovarian Cancer

status: Public on Apr 01 2017

first: Ilya

last: Korsunsky

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Brigham and Women's Hospital

summary: MicroRNAs have been established as key regulators of tumor gene expression and as prime biomarker candidates for clinical phenotypes in epithelial ovarian cancer (EOC). We analyzed the coexpression and regulatory structure of microRNAs and their colocalized gene targets in primary tumor tissue of 20 advanced epithelial ovarian cancer patients in order to construct a regulatory signature for clinical prognosis. We performed an integrative analysis to identify two prognostic microRNA/mRNA coexpression modules, each enriched for consistent biological functions. One module, enriched for malignancy related functions, was found to be upregulated in malignant versus benign samples. The second module, enriched for immune related functions, was strongly correlated with intratumoral immune infiltrates of T cells, NK cells, Cytotoxic Lymphocytes, and Macrophages. We validated the prognostic relevance of the immunological module microRNAs in the publically available TCGA dataset. These findings provide novel functional roles for microRNAs in the progression of advanced EOC and possible prognostic signatures for survival.

overall_design: 26 samples from Primary EOC tumor and 13 samples from benign Ovarian masses were assayed.


title: Comprehensive evaluation of genome-wide 5-hydroxymethylcytosine profiling approaches in human DNA [HumanMethylation450]

type: Methylation profiling by genome tiling array


title: RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)

status: Public on Mar 27 2017

city: Stuttgart

first: Joana

middle: Danica

last: Simen

address: Allmandring 31

department: Institute of Biochemical Engineering

institute: University of Stuttgart

summary: In large-scale production processes, metabolic control is typically achieved by limited supply of essential nutrients like glucose or ammonia. With increasing bioreactor dimensions, microbial producers such as Escherichia coli are exposed to changing substrate availabilities due to limited mixing. In turn, cells sense and respond to these dynamic conditions leading to frequent activation of their regulatory programs. Previously, we characterized short- and long-term strategies of cells to adapt to glucose fluctuations. Here, we focused on fluctuating ammonia supply, while studying a continuously running two-compartment bioreactor system comprising a stirred tank reactor (STR) and a plug flow reactor (PFR). Genes were repeatedly switched on/off when E. coli returned to the STR. Moreover, E. coli revealed highly diverging long-term transcriptional responses in ammonia compared to glucose fluctuations. The identification of target genes may help to create robust cells and processes for large-scale application.

overall_design: mRNA time profiles of E. coli K12 W3110 ammonia-limited chemostat STR-PFR culture:  59 samples derived from STR or different PFR sample ports over process time including three samples derived from the reference steady state before PFR addition,  in duplicate, generated using Illumina HiSeq 2500.

middle: D

first: Michael

last: Löffler

first: Jakob

last: Matthes

first: Günter

last: Jäger

first: Karin

last: Schäferhoff

first: Ralf

last: Takors


title: IPTG-induced CRISPRi repression of firefly luciferase in Streptococcus pneumoniae

status: Public on Mar 03 2017

city: Groningen

first: Jelle

last: Slager

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

summary: Genome-wide screens have discovered a large set of essential genes in the human pathogen Streptococcus pneumoniae. However, the function of many essential genes is still unknown, hampering vaccine and drug development programs. Based on results from transposon-sequencing (Tn-Seq), we refined the list of essential genes in S. pneumoniae serotype 2 strain D39. Next, we created a knockdown library targeting all 391 potentially essential genes using CRISPR interference (CRISPRi). Using high-content microscopy screening, we searched for essential genes of unknown function with clear phenotypes in cell morphology upon CRISPRi-based depletion. We identified SPD1416 and SPD1417 (named to MurT and GatD, respectively) as essential peptidoglycan synthesis proteins and we show that SPD1198 and SPD1197 (named to TarP and TarQ, respectively) are responsible for the polymerization of teichoic acid (TA) precursors. This knowledge enabled us to reconstruct the unique pneumococcal TA biosynthetic pathway. Our CRISPRi library provides a valuable tool for characterization of pneumococcal genes and pathways and revealed several promising antibiotic targets. This RNA-Seq dataset is aimed to show that induction of the CRISPRi system very selectively represses its target gene, firefly luciferase, without other observable transcriptional effects.

overall_design: Pairwise comparison of control and IPTG-induced cells (RNA-seq), analyzing the effect of CRISPRi activation on the transcriptome of Streptococcus pneumoniae. It was performed with deep sequencing, using an Illumina HiSeq 2000 machine with 51 nt single-end reads. Samples were analysed from duplicate samples. To separate CRISPRi-specific effects from general IPTG-induced effects, we compared the uninduced strains with IPTG-induced strains that either did or did not contain the single-guide RNA.

first: Xue

first: Clément

last: Gallay

first: Morten

last: Kjos

first: Arnau

last: Domenech

first: Sebastiaan

middle: P

last: van Kessel

first: Kèvin

last: Knoops

first: Robin

last: Sorg

first: Jing-Ren

first: Jan-Willem

last: Veening


title: HSF1-dependent and -independent regulation of the mammalian in vivo heat shock response and its impairment in Huntington’s disease

city: Cambridge

first: David

last: Housman

address: 500 Main St

department: Biology

institute: MIT

summary: The heat shock response (HSR) is a mechanism to cope with proteotoxic stress by inducing the expression of molecular chaperones and other heat shock response genes. The HSR is evolutionarily well conserved and has been widely studied in bacteria, cell lines and lower eukaryotic model organisms. However, mechanistic insights into the HSR in higher eukaryotes, in particular in mammals, are limited. We have developed an in vivo heat shock protocol to analyze the HSR in mice and dissected heat shock factor 1 (HSF1)-dependent and -independent pathways. Whilst the induction of proteostasis-related genes was dependent on HSF1, the regulation of circadian function related genes, indicating that the circadian clock oscillators have been reset, was independent of its presence. Furthermore, we demonstrate that the in vivo HSR is impaired in mouse models of Huntington’s disease but we were unable to corroborate the general repression of transcription after a heat shock found in lower eukaryotes.

overall_design: RNA-Seq was performed on mRNA isolated from quadriceps femoris muscle of 24 mice. These mice were of wild type, R6/2, and Hsf1-/- genotypes. Two mice of each genotype were tested in four conditions: (1) heat shock, (2) control heat shock, (3) HSP90 inhibition (NVP-HSP990), and (4) HSP90 inhibition vehicle.

first: Andreas

last: Neueder

first: Theresa

last: Gipson


title: PARP3 is a promoter of chromosomal rearrangements and limits G4 DNA

status: Public on Mar 01 2017

city: Brookline

first: Tovah

last: Day

address: 450 Brookline Avenue

institute: Dana Farber Cancer Institute

summary: Chromosomal rearrangements are essential events in the pathogenesis of both malignant and nonmalignant disorders, yet the factors affecting their formation are incompletely understood.  We developed a zinc finger nuclease translocation reporter (ZITR) and screened for factors that modulate rearrangements in human cells.  We identified UBC9 and RAD50 as suppressors and 53BP1, DDB1, and PARP3 as promoters of chromosomal rearrangements across human cell types.  We focused on poly(ADP)ribose polymerase 3 (PARP3) as it is dispensable for murine viability and has druggable catalytic activity.  We found that PARP3 regulated G quadruplex (G4) DNA in response to DNA damage, which suppressed repair by nonhomologous end-joining and homologous recombination.  Chemical stabilization of G4 DNA in PARP3-/- cells led to widespread DNA double-strand breaks and synthetic lethality.  We propose a model in which PARP3 suppresses G4 DNA and facilitates DNA repair by multiple pathways.

overall_design: RNA-seq was performed on WT and PARP3-/- A549 cells with vehicle treatment or treatment with 1 micromolar pyridostatin.  All conditions were performed in biological triplicate.

last: Weinstock


title: Analysis of the transcriptional changes dependent on miR-155 expression without and with therapeutic pressure

city: Heidelberg

first: Maximilian

middle: Georg

last: Schliesser

address: INF 280

institute: DKFZ

summary: Expression profiling by Illumina gene expression microarrays

overall_design: control and miR-155 overexpressing T98G without and with chemo- and radiotherapy

middle: G

first: Wolfgang

last: Wick


title: Diverse Non-Genetic Allele Specific Expression Effects Shape Genetic Architecture at the Cellular Level in the Mammalian Brain

status: Public on Feb 28 2017

city: Salt Lake City

first: Christopher

last: Gregg

state: Utah

address: 323 Wintrobe Bldg 530, 20 North 1900 East

department: Neurobiology and Anatomy

institute: University of Utah

sample_organism:
Macaca fascicularis
Mus musculus

platform_organism:
Macaca fascicularis
Mus musculus


title: Transcriptome analysis of Streptococcus gallolyticus subsp. gallolyticus in interaction with THP-1 macrophages [BAA-2069 5h]

first: Imke

last: Grimm

overall_design:
Analysis of two S. gallolyticus subsp. gallolyticus strains (BAA-2069 and UCN 34) at three different time points (-60min; 0h and 5h) of phagocytosis. For each time point and strain three biological replicates were taken and normalized on the -60min-timepoint.

This series contains 3 re-analyzed samples from GSE96822 (GSM2544657, GSM2544659, and GSM2544661).

first: Tanja

last: Vollmer

first: Jens

last: Dreier


title: Transcriptome analysis of Streptococcus gallolyticus subsp. gallolyticus in interaction with THP-1 macrophages [UCN 34 0h]

overall_design: Analysis of two S. gallolyticus subsp. gallolyticus strains (BAA-2069 and UCN 34) at three different time points (-60min; 0h and 5h) of phagocytosis. For each time point and strain three biological replicates were taken and normalized on the -60min-timepoint.


title: Diverse Non-Genetic Allele Specific Expression Effects Shape Genetic Architecture at the Cellular Level in the Mammalian Brain [HybridMouseDRN]

summary: Determine allele level expression in hybrid mice of different ages

overall_design: RNASeq - HybridMouseDRN

first: Chris

first: Elliott

last: Ferris


title: Regulation of nucleosome positioning by a CHD Type III chromatin remodeller and its relationship to developmental gene expression in Dictyostelium [MNase-seq]

status: Public on Feb 26 2017

city: Oxfors

first: James

last: Platt

address: Roosevelt Drive

institute: University of Oxford

summary: We utilized MNase-seq to profile nucleosome positions in wild type (Ax2) and ChdC null cells both in growing cells and a partially developed state (loose-mound) to study changes in nucleosome positioning and occupancy during development and the impact the deletion of ChdC an ATP-dependent chromatin remodeller has on nucleosome positioning and occupancy. As a control for MNase sequence bias we also digested naked DNA with MNase.

overall_design: Studying nucleosome positions in wild type and ChdC mutant cells

middle: L


title: Influence of temperature fluctuations during cryopreservation on vital parameters, plasticity, and transgene expression of placental multipotent stromal cells

city: Hannover

first: Denys

last: Pogozhykh

address: Carl-Neuberg-Str. 1

department: Institute for Transfusion Medicine

institute: Hannover Medical School

summary: In this study we performed comprehensive analysis of changes in cell survival, vital parameters, plasticity, as well as transgene expression of placental MSCs after temperature fluctuations within the liquid nitrogen steam storage, mimicking long-term preservation in practical biobanking, transportation, and temporal storage. It was shown that viability and metabolic parameters of placental MSCs did not significantly differ after temperature fluctuations in the range from  -196ºC to  -100ºC in less than 20 cycles in comparison to constant temperature storage. However, increasing of the temperature range to  -80ºC as well as increasing the number of cycles, leads to significant lowering of these parameters after thawing. The number of apoptotic changes increases depending on the number of cycles of temperature fluctuations. Besides, adhesive properties of the cells after thawing are significantly compromised in the samples subjected to temperature fluctuations during storage. Plasticity of placental MSCs was not compromised neither after cryopreservation with constant end temperatures nor with temperature fluctuations. However, regulation of various genes after cryopreservation procedures significantly varies. Alterations in structural and functional parameters of placental MSCs after long-term preservation should be considered in practical biobanking due to potential temperature fluctuations in samples. At the same time, plasticity and transgene expression are not compromised during studied storage conditions, while certain gene regulation is observed.

overall_design: Part of the samples was cryopreserved with the constant end temperature, while the other part of the samples was subjected to repeated temperature fluctuations between -80ºC and -196ºC during cryopreservation. After thawing the samples were differentiated into three mesenchymal lineages with the following comparative evaluation of gene regulation. Five dual-colour microarrays were processed. Each sample was tested once.

first: Olena

first: Thomas

last: Mueller


title: Comprehensive evaluation of genome-wide 5-hydroxymethylcytosine profiling approaches in human DNA

first: Ksenia

last: Skvortsova

overall_design: Refer to individual Series


title: The dentate gyrus after traumatic brain injury [miRNA]

status: Public on Feb 25 2017

city: Kuopio

first: Asla

last: Pitkänen

address: P.O.B. 1627 (Neulaniementie 2)

department: Department of Neurobiology

country: Finland

institute: University of Eastern Finland

summary: Analysis of the dentate gyrus of traumatic brain injury model. Results provide insight into the molecular mechanism underlying TBI.

overall_design: This study was designed to estimate changes in miRNA expression levels after lateral fluid-percussion injury as a model of TBI.

first: Noora

last: Puhakka

first: Anna

last: Bot

first: Niina

last: Vuokila

first: Konrad

last: Dębski

first: Katarzyna

last: Lukasiuk


title: The dentate gyrus after traumatic brain injury

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

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


title: Differentially expressed genes and chromosomal alterations in ovarian cancer cell lines sensitive or resistant to a Src-inihibitor, saracatinib

status: Public on Mar 05 2017

city: Aurora

first: Ichiro

last: Nakachi

state: CO

address: 12700 East 19th Avenue, RC2 9th floor

department: Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine

institute: University of Colorado Denver

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

summary:
We sought to detect predictive markers related to a Src kinase inhibitor (saracatinib) sensitivity in ovarian cancer. Cell proliferation assays assigned 18 ovarian cancer cell lines to sensitive or resistant to this drug.
Using baseline gene expression data from these 18 cell lines, we sought to identify differentially expressed genes correlated with saracatinib sensitivity. We also used SNP array data from 7 cell lines to detect differentically affected genomic locations.

overall_design: Affymetrix Human Gene 1.0 ST arrays were used for 18 ovarian cancer cell lines. Copy number analysis with Affymetrix SNP 6.0 arrays was performed for 7 ovarian cancer cell lines.

first: Christopher

last: Coldren

first: Robert

last: Stearman

first: Barbara

last: Helfrich

first: Monique

last: Spillman


title: Transcriptome analysis of Streptococcus gallolyticus subsp. gallolyticus in interaction with THP-1 macrophages [BAA-2069 0h]

first: Imke

last: Grimm

address: Georgstraße 11

institute: Herz- und Diabeteszentrum NRW; Universitätsklinikum der Ruhr-Universität Bochum

first: Tanja

last: Vollmer

first: Jens

last: Dreier


title: Expression data from human T cell populations

status: Public on Feb 24 2017

city: Gent

first: Bart

last: Vandekerckhove

address: MRB2 1e verdieping, De Pintelaan 185

department: Department of Clinical chemistry, Microbiology and immunology

country: Belgium

institute: Ghent University

summary:
Murine T cell populations have been described that are generated upon strong TCR activation, a process referred to as agonist selection. This murine population is phenotypically and functionally characterized and lacks coreceptors CD4 and CD8 (double negative or DN). The existence of a human equivalent of this population is not clear.
We identified a population based on expression of PD-1, CD10 and lower expression of CD3 that shows characteristics resemblant of mouse DN T cells. Here, we perform transcriptional profiling of this particular PD-1+ T cell population in human thymus and cord blood and compare it to conventional CD8 T cells (that are PD-1 negative) as well as innate TCRgammadelta+ T cells.

overall_design: We purified PD-1- CD8+and PD-1+CD8+ populations from human donor post-natal thymus and cord blood as well as TCRgd+T cells from human post-natal thymus. Purification was based on ex vivo fluorescence-activated cell sorting (FACS) of mononuclear cell fractions obtained from donor samples. For each population 3 donors were used and obtained fractions were pooled for further analysis.

first: Greet

last: Verstichel


title: The dentate gyrus after traumatic brain injury [mRNA]

overall_design: This study was designed to estimate changes in gene expression levels after lateral fluid-percussion injury as a model of TBI.


first: Maximilian

last: Schliesser

summary: CpG island methylation profiling of anaplastic gliomas compared to healthy control. Goal was to identify anaplastic glioma-specific differentially methylated regions (DMRs).

overall_design: Highly methylated DNA from cases and controls was enriched by methyl CpG-immunoprecipitation (MCIp) and co-hybridized. DMRs were defined by stepwise stringent criteria such as selecting top 5% vicinal array probes only. Anaplastic glioma specific DMRs were identified.

first: Wolfgang

last: Wick


title: Detectable clonal mosaicism in blood as biomarker of cancer risk in Fanconi anemia

city: Barcelona

first: Luis Alberto

middle: Perez

last: Jurado

state: Barcelona

address: Doctor Aiguader, 88 (PRBB)

department: Department of Experimental and Health Sciences

country: Spain

institute: Universitat Pompeu Fabra

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

summary: Detectable clonal mosaicism for large chromosomal events has been associated with aging and increased risk of hematological and some solid cancers. We hypothesized that genetic cancer predisposition disorders such as Fanconi anemia (FA) could manifest a high rate of chromosomal mosaic events (CMEs) in peripheral blood, which could be used as early biomarkers of cancer risk. We studied the prevalence of CMEs by Single-Nucleotide Polymorphism (SNP) array in 130 FA patients’ blood DNA and their impact on cancer risk. We detected 51 CMEs (4.4-159Mb in size) in 16/130 patients (12.3%), 9 of them with multiple CMEs. Most frequent events were gains at 3q (n=6) and 1q (n=5), both previously associated with leukemia, as well as rearrangements with breakpoint clustering within the Major Histocompatibility Complex (MHC) locus (p=7.3x10-9). Compared to 15743 age-matched population controls, FA patients had 126-140 higher risk of detectable CMEs in blood (p<2.2x10-16). Prevalent and incident hematologic and solid cancers were more common in CME carriers (OR=11.6, CI95%=3.4-39.3, p=2.8x10-5), leading to poorer prognosis. The age-adjusted hazard risk (HR) of having cancer was almost 5 times higher in FA individuals with CMEs than in those without CMEs. Regarding survival, the HR of dying was 4 times higher in FA individuals having CMEs (HR=4.0, CI95%=2.0-7.9, p=5.7x10-5). Therefore, our data suggests that molecular karyotyping with SNP arrays in easy-to-obtain blood samples could be used for better monitoring of bone marrow clonal events, cancer risk and overall survival of FA patients.

overall_design: To establish detectable clonal mosaicism prevalence in Fanconi Anemia (FA) patients we analyzed peripheral blood samples from 130 patients by using different Illumina SNP array platforms. A total amount of 17 samples were analyzed by Illumina Human 1M-Duov3, 96 samples by Illumina OmniExpress-12 v1.0 (730K), 1 sample by Illumina HumanOmniExpressExome- 8v1.2 (960K) and 16 samples Illumina Human Core-12v1-0-B (250k).

first: Luis

last: Pérez-Jurado

first: Jordi

last: Surrallés


title: Porphyromonas gingivalis transcriptome in presence or absence of pABA

status: Public on Feb 18 2017

city: Seattle

first: David

middle: A. C.

last: Beck

state: WA

address: Benjamin Hall IRB, Rm 440, UW Box 355014

department: ChemE & eScience Institute

institute: University of Washington

summary: We report the results of high throughput sequencing on P. gingivalis cells in the presence or absence of 4 aminobenzoate/para-amino benzoic acid (pABA)

overall_design: Examination of Pg incubated for 18 hours with pABA or vehicle control

first: Masae

last: Kuboniwa

first: Erik

last: Hendrickson

first: Qian

last: Wang

first: Aktuo

last: Sakanala

first: Tiansong

first: Daniel

last: Miller

first: Marvin

last: Whiteley

first: Atsuo

last: Amano

first: Huizhi

first: Murray

last: Hackett

first: Richard

last: Lamont


title: RNA-sequencing of murine norovirus (MNV) infection and loxoribine (Lox) stimulation in RAW264.7 macrophages

status: Public on Feb 14 2017

first: Peter

last: White

address: High Street

institute: University of New South Wales

summary: This study aimed to generate a comprehensive analysis of changes in the transcriptome following MNV infection. Furthermore, we aimed to perform a differential gene expression analysis between MNV infection and loxoribine (tlr7 agonist) treatment to delineate features of the host modified directly by the MNV as opposed to indirect changes induced through IFN signalling.

overall_design: Transcript expression profiles of RAW264.7 cells mock infected, infected with MNV (MOI 5) or treated with loxoribine (1 mM) for 12 hrs were generated using Illumina NextSeq500.

middle: E

last: Tuipulotu


title: Transcriptional profiles of PBMCs from pigs infected with three genetically diverse PRRSV strains

status: Public on Feb 23 2017

city: Pulawy

first: Magdalena

last: Materniak-Kornas

address: Partyzantow 57

department: Biochemistry

country: Poland

institute: National Veterinary Research Institute

summary: Porcine reproductive and respiratory syndrome virus (PRRSV) is a causative agent of an important infectious disease causing serious economic losses to swine industry called PRRS (porcine reproductive and respiratory syndrome). The clinical signs of this syndrome indcude respiratory disorders, abortions and variable mortality in piglets. To compare the virulence of highly diverse East European strains belonging to subtype 2 (Russian strain ILI and Belarusian strain BOR) and Danish strain from classical subtype 1 (DAN) the experimental study enrolling infection of piglets was performed. Gene expression profiles of peripheral blood mononuclear cells (PBMC) of piglets infected with three PRRSV strains vs control piglets were analysed by microarray analysis to gain insight into transcriptome changes after PRRSV infection.

overall_design: Three groups of 8 weeks old pigs were infected with a PRRSV Type 1 strains including subtype 1 strain 18794 (DAN), Russian isolate ILI6 (ILI) and Belarusian isolate BOR59 (BOR). Pigs were inoculated intranasally with 2 ml of respective virus inoculum. Negative control group was sham-inoculated with 2 ml of Eagle’s medium.Blood samples were collected from 5 randomly selected pigs per each group at 7 days post infection (dpi) and submitted for peripheral blood mononuclear cells  (PBMC) isolation. RNA was extracted from PBMSs of each animal using RNeasy Kit (Qiagen). RNA of 5 animals from each group were pooled in 4 groups: DAN, ILI BOR and control, for microarray experiment. Each pool was processed in 4 repeats using Two-Color Microarray-Based Gene Expression Analysis.

first: Marzena

last: Rola-Łuszczak

first: Aneta

last: Pluta

first: Katarzyna

last: Podgórska

first: Jens

last: Nielsen

first: Tomasz

last: Stadejek

first: Jacek

last: Kuźmak


title: Small RNA libraries from pooled synthetic miRNAs

status: Public on Feb 16 2017

first: Kai

address: 401 Terry Ave N

institute: Institute for Systems Biology

summary: A total of 286 synthetic miRNAs that are commonly observed in circulation were synthesized by Integrated DNA Technologies (Coralville, IA).

overall_design: We randomly assigned synthetic miRNAs to each of three plates (Plate 1, Plate 2, and Plate 3) respectively. Six combinations of different concentrations from these three synthetic miRNAs plates were subjected to small RNA sequencing.

first: David

last: Baxter

first: Kelsey

last: Scherler


title: Foxa2 identifies a novel ventricular-specific cardiac progenitor population during gastrulation.

status: Public on Feb 08 2017

city: New York

first: Andrew

last: Sharp

state: NY

address: 1470 Madison Av

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: The recent identification of novel progenitor populations that contribute to the developing heart in a distinct temporal and spatial manner has fundamentally improved our understanding of cardiac development. However, little remains known about cardiac specification events prior to the establishment of the heart tube, or the mechanisms that direct atrial versus ventricular specification. We have identified a novel progenitor population that gives rise specifically to cardiovascular cells of the ventricles but not the atria, and to the epicardium of the differentiated heart. We determined that this cell population is first specified during gastrulation, when it transiently expresses Foxa2, a gene not previously implicated in cardiac development. Using chimeric mosaic analysis we further demonstrate that Foxa2 is cell-autonomously required for the development of ventricular cells. Finally, we reveal the existence of an analogous Foxa2+ cardiac mesoderm population during in vitro differentiation from embryonic stem cells and illustrate that these cells express genes relevant for heart development. Our data thus describe the first progenitor population identified as early as gastrulation that displays ventricular-specific differentiation potential. Together, these findings provide important new insights into the developmental origin of ventricular and atrial myocytes, and will lead to the establishment of new strategies for generating these cell types from pluripotent stem cells.

overall_design: Examination of global gene expression in four different cell types

first: Evan

last: Bardot

first: Damelys

last: Calderon

first: Francis

last: Santoriello

first: Songyan

last: Han

first: Kakit

last: Cheung

first: Bharati

last: Jadhav

first: Ingo

last: Burtscher

first: Heiko

last: Lickert

first: Valerie

last: Gouon-Evans

first: Nicole

middle: C

last: Dubois


title: RNA-sequencing of longitudinal murine norovirus (MNV) infection in RAW264.7 mouse macrophages

city: Sydney

first: Peter

last: White

summary: The transcriptome has an abundance of information about the function of individual cells, tissues and an organism in general. Characterising the transcriptome of virus infected cells can illuminate features of the viral-host relationship that are important for pathogenesis. This study broadly aimed to quantify the host gene expression changes that occur following MNV infection. Furthermore, we  aimed to identify alterations in specific biological pathways by identifying alterations in transcript abundance that increase or decrease in intensity with MNV infection over time.

overall_design: Transcript expression profiles of RAW264.7 cells mock infected or infected with MNV for 4, 8, 12, 16 and 20 hours (MOI 5) were generated by RNA-sequencing using Illumina NextSeq500.

first: Daniel

last: Tuipulotu


title: Diverse Non-Genetic Allele Specific Expression Effects Shape Genetic Architecture at the Cellular Level in the Mammalian Brain [Primate Daughters]

first: Christopher

last: Gregg

summary: Align offspring RNASeq reads to unbiased transcriptomes made incorporating parent genotype information

overall_design: RNASeq - 10 daughters

first: Chris

first: Elliott

last: Ferris


title: Characterization of mouse embryonic stem cells without any G1 cyclins

status: Public on Feb 07 2017

city: Boston

first: Lijun

last: Liu

address: 450 brookline Ave

summary: We performed regular RNA-seq to understand G1 cyclins function in ES cells

overall_design: Regular RNA-seq was performed for in wild-type ES cells and ES cells without any G1 cyclins (called Q-KO ES cells)

last: Sicinski


title: Diverse Non-Genetic Allele Specific Expression Effects Shape Genetic Architecture at the Cellular Level in the Mammalian Brain [Primate Parents]

summary: Genotype parent macaques. This allows us to distinguish maternal and paternal expression in the transicriptomes from the offspring. This also allows us to create a transcriptome index  for each daughter that reflects the possible heterozygous SNPs  wiith IUPAC codes.  This then allows for an alignment that is not biased towords the maternally or paternally expressed reads.

overall_design: Whole genome sequencing


title: Gene expression profiling in MCF-7 cells overexpressing distal-less homeobox 2 (Dlx-2)

status: Public on Feb 13 2017

city: Pusan

first: Ho Sung

last: Kang

address: 30, Jangjeon-dong

department: Departmemt of Molecular Biology

institute: Pusan National University

summary: Gene expression profiling of MCF-7 cells that transfected with Dlx-2

overall_design: Gene expression levels were determined by comparing the gene expression of the experimental samples (transfected with Dlx-2) with that of the control sample (transfected with mock).

first: H


title: Experimentally induced thiamine deficiency in neuronally differentiated SH-SY5Y cells using oxythiamine

status: Public on Feb 06 2017

city: San Juan

first: Nataliya

last: Chorna

state: Puerto Rico

address: School of Medicine

institute: University of Puerto Rico

summary: Our results provide a new information of the specific action of oxythiamine on the signaling processes of apoptosis that can apply for the development of new experimental cellular models of neurodegenerative diseases.

overall_design: Human SH-SY5Y neuroblastoma cell line differentiated with all trans retinoic acid (ATRA) for 72 h were followed by treatment with oxythiamine for an additional 72 h. Cells non-treated with oxythiamine were examine as control. Gene expression profiling was performed using Atlas Human Apoptosis Array (Cat. #7743-1) (BD Biosciences Clontech).

first: Sergiy

last: Chornyy


title: Regulation of nucleosome positioning by a CHD Type III chromatin remodeller and its relationship to developmental gene expression in Dictyostelium [RNA-seq]

first: James

last: Platt

summary: We utilized RNA-seq to profile expression levels in wild type Ax2 cells and a mutants for ChdC a member of a family of ATP-depedent chromatin remodellers in Dictyostelium discoideum. Total RNA was polyA enriched and sequenced at two stages of development: in the growth stage (0H) and loose mound stage of development (10-12H)

overall_design: Looking at mRNA levels in Ax2 and chdC- cells


title: Integrated transcriptomic and metabolomic to characterize cold stress response in Nicotiana tabacum

status: Public on Jan 30 2017

city: singapore

first: JINGJING

last: JIN

address: singapore

country: Singapore

institute: Temasek LifeScience Laboratory

summary: We checked the difference of CB-1 and K326 by transcriptomic and metabolomic analysis and found some important genes related to cold stress

overall_design: 4 RNA-seq samples for CB-1 and K326 of WT and cold treatment

first: Jingjing

last: Jin

first: Peijian

last: Cao


title: Quantitative Transcriptome Analysis of the Stomach Neck Mucosa from Control vs Claudin (CLDN)-18 knockout mice.

status: Public on Jan 19 2017

first: Susan

last: Hagen

state: Massachusetts

address: 330 Brookline Avenue, E/RW-871

department: Surgery

institute: Beth Israel Deaconess Medical Center

summary:
Purpose:  To determine early changes in gene expression that drive gastric cancer development in the landscape of CLDN18 loss using RNAseq.
Results:  Although claudin-18 is a tight junction protein and should regulate paracellular permeabiity and/or ion flux across the mucosa, we showed this protein is rather a potent tumor suppressor that regulates cellular signaling and differentiation pathways in gastric epithelial cells.
Methods: Stomach neck region mRNA profiles of 7-day-old wild-type (WT) and claudin-18 knockout (CLDN18−/−) mice were generated by deep sequencing, in triplicate, using the Illumina HiSeq2000 sequencing system. The resulting sequences were mapped to the Mouse genome (mm10) using STAR aliger and P-values were adjusted using the Benjamini-Hochberg procedure (J R Statist Soc B  1995;57:289-300).
Conclusions:  Loss of claudin-18 promotes gastric cancer development by modulating the expression program of gastric epithelial cells, including cellular signaling and differentiation pathways that are required for mucosal homeostasis.

overall_design: Stomach (neck region only) mRNA profiles of 7-day old wild-type (WT) and CLDN18-/- mice were generated by deep sequencing, in triplicate, using an Illumina HiSeq2000 sequencing system.

first: Yaoyu

last: Wang


title: Plant response to chitin 4mer

status: Public on Feb 17 2017

city: Madrid

first: Marta

last: Berrocal-Lobo

state: Madrid

address: Antonio Nováis 10, s/n

department: System and Natural Resources

institute: School of Forestry Engineering and Natural Resources

summary:
Analysis of 14-day-old Columbia-0 seedlings treated with chito-tetramer.Results provide insight into the signaling pathways involved in plant devlopment in response to the four-mer.
Chitin is the second biopolymer most abundant at nature, after cellulose, forming part of insect exosqueletons, crustacean shells, krill and fungal spores where is present as a high molecular weight molecule. Previously we showed that Arabidopsis defense related clusters of genes were induced by high molecular weight chitin (CHH) or 8mer oligosaccharides similarly (Ramonell et al., 2005), some of those genes were essential for effective defense against phytopathogenic fungus (Berrocal-Lobo et al., 2010). At this work we show that differentially, a chitin oligosaccharide of lower molecular weight (4mer), induce genes in Arabidopsis related principally to vegetative growth, development and carbon and nitrogen metabolism.

overall_design: 3 samples treated by the 4mer and 3 control samples

first: Katrina

last: Ramonell

first: Shauna

last: Somerville


title: Genome-wide high-resolution SNP-array analysis of childhood melanocytic tumor with ambiguous histopathological features

status: Public on Feb 01 2017

first: Jeffrey

last: Zhao

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

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

summary: In our clinical practice, we perform genome-wide high-resolution SNP-array analysis as an adjunct to the histopathologic diagnosis for diagnostically challenging melanocytic tumors. The concept of using array-based DNA copy number analysis to screen for gene fusions associated with unbalanced genomic aberrations flanking the fusion points was applied in the diagnostic setting, and intragenic copy number changes involving common receptor kinase genes are typically further analyzed and, if necessary, studied by alternative methods. Here we present the discovery of recurrent NTRK3 gene rearrangements in childhood melanocytic neoplasms based on genome-wide high-resolution SNP-array analysis.

overall_design: Affymetrix Oncoscan arrays were performed according to the manufacturer's directions on DNA extracted from paraffin embedded formalin fixed tumor tissues from 4 childhood melanocytic tumors.  Genome-wide DNA copy number alterations and allelic imbalances were analyzed.

first: Lu


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and L2hgdh-/- mice brain Transcriptomes

status: Public on Feb 20 2017

city: La Jolla

first: Shenghong

last: Ma

state: CA

address: 2880 TORREY PINES SCENIC DR, Sanford Consortium

institute: UCSD

summary: We report the transcriptional difference of L2hgdh gene knock out mice brain with wild type control using RNA-seq technology.

overall_design: brain mRNA profiles of 2-month old wild type and L2hgdh knock out mice

first: Renqiang

last: Sun


title: NGS and Transcriptome Analyses using AZ customized microarray on Leaf Abscission zone in Tomato (Solanum lycopersicum) Plants

city: Bet-Dagan

first: Srivignesh

last: Sundaresan

state: Israel

address: P.O.Box 6, Bet- Dagan

department: Post Harvest Technology

country: Israel

institute: Agricultural Research Organisation, The volcani center, Israel

summary: To extend our previous knowledge from our gene expression studies on Leaf Abscission zone using Affymetrix microarray chip we have employed whole transcriptome analysis by NGS as a discovery platform to identify and add the transcripts to pre-existing database. We designed the Customized AZ Microarray chip with the transcripts obtained from NGS (includes novel transcripts), pre existing Agilent probes, and some additional transcripts from previous databases. The leaf AZ tissue was sampled at five time points (0, 24, 48, 72, and 96 h), following leaf deblading and ethylene (10ppm) treated for 24h and analyzed for their gene expression profiles using the customized AZ microarray.

overall_design: Solanum lycopersicum Custom Microarray 4x180K Array designed by Genotypic Technology Private  Limited. (AMADID:043310)

first: Sonia

last: Philosoph-Hadas

first: Amnon

last: Lers

first: Shimon

last: Meir


title: NGS and Transcriptome Analyses using AZ customized microarray on Flower Abscission zone in Tomato (Solanum lycopersicum) Plants

summary: To extend our previous knowledge from our gene expression studies on Flower Abscission zone using Affymetrix microarray chip we have employed whole transcriptome analysis by NGS as a discovery platform to identify and add the transcripts to pre-existing database. We designed the Customized AZ Microarray chip with the transcripts obtained from NGS (includes novel transcripts), pre existing Agilent probes, and some additional transcripts from previous databases. The flower AZ tissue was sampled at five time points (0, 2, 4, 8, and 14 h), following flower removal and analyzed for their gene expression profiles using the customized AZ microarray.


title: Genes Associated with MUC5AC Expression in the Human Airway Epithelium

status: Public on Feb 09 2017

first: Yael

last: Strulovici-Barel

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

summary: To help define the genes associated with mucus synthesis and secretion in the human small airway epithelium, we hypothesized that comparison of the transcriptomes of the small airway epithelium of individuals that express high vs low levels of MUC5AC, a major secretory mucin and the major component of airway mucus, could be used as a probe to identify the genes related to human small airway mucus production / secretion.   Genome-wide comparison between healthy nonsmokers grouped as “high MUC5AC expressors” vs “low MUC5AC expressors” identified significantly up-regulated and  down-regulated genes in the high vs low expressors. Based on the literature, genes in the up-regulated list were used to identify a 73 “MUC5AC-associated core gene” list with 9 categories: mucus components; mucus-producing cell differentiation-related transcription factor; mucus-producing cell differentiation-related pathway or mediator; post-translational modification of mucin; vesicle transport; endoplasmic reticulum stress-related; secretory granule-associated; mucus secretion-related regulator and mucus hypersecretory-related ion channel.  The identification of the genes associated with increased small airway mucin production in humans should be useful in identifying therapeutic targets to treat small airway mucus hypersecretion.

overall_design:
Since airway surface epithelial cells are the sole local source of mucus in the small airways, which are devoid of submucosal glands and mucus contributes to the morbidity and mortality of  smoking-related lung diseases, especially chronic obstructive pulmonary disease (COPD), we sought to define the genes associated with mucus synthesis and secretion in the human small airway epithelium.  Microarray analysis revealed 528  up-regulated and 15 down-regulated genes in MUC5AC high expressors compared to the MUC5AC low expressors. From 528 up-regulated genes, we found 73 genes with literature supported roles or potential roles in mucus production / secretion. These MUC5AC-core genes suggest that multiple molecular events involving the nucleus, endoplasmic reticulum, Golgi, vesicles and plasma membrane work coordinately in the human small airway epithelium to promote mucus production and secretion in MUC5AC-producing cells. The identification of the genes associated with increased small airway mucin production in humans should be useful in identifying therapeutic targets to treat small airway mucus hypersecretion.

Samples' MUC5ACexpression status provided in supplementary file linked below.

*** Note: Processed data not provided for ~86 Samples.

first: Guoqing

first: Zhibo

last: Xu

first: Rui

first: Mohammed

last: Al-Hijji

first: Jacqueline

last: Salit

first: Ann

last: Tilley

first: Jason

last: Mezey

first: Ronald

last: Crystal


title: Gene expression in HT-29-MTX intestinal epithelial cells treated with Ancylostoma ceylanicum hookworm larvae

status: Public on Jan 14 2017

city: Ithaca

first: Caitlin

last: Feather

address: Riley-Robb Hall, Wing Dr

department: Biological and Environmental Engineering

institute: Cornell University

summary: HT-29-MTX cells were treated with Ancylostoma ceylanicum hookworm larvae or left untreated.  The differences in gene expression between treated and untreated samples was observed.

overall_design: HT-29-MTX cells were grown for 7 days post-confluency (total 21 days) and were either treated with iL3 A. ceylanicum larvae for 24 hours or left untreated.  RNA from treated and untreated samples was collected and differences in gene expression were observed using RNA-Seq.

first: John

last: March


title: 809094 Biomarker Identification in Fracture Healing (experiment #3808 miRNA)

status: Public on Jan 11 2017

city: Philadelphia

first: Annamarie

last: Horan

state: PA

address: 3737 Market Street, 6th Floor

department: Orthopaedic Surgery

institute: University of Pennsylvania

summary:
The specific genes that distinguish normal fracture healing from abnormal healing or nonunion in humans are unknown. This study explored global RNA expression in remnant bone fragments from acutely injured patients undergoing open primary fracture repair surgery. These data will be compared to blood samples collected from acutely injured subjects, chronic nonunion subjects, and a panel of healthy volunteers.
We used microarrays to do a global comparison across bone fragments collected from different patients, and different bones. We also evaluated the role of remnant bone preparation which was either immediate freezing in liquid nitrogen or heat stabilized with the Denator Stabilizer(TM) system.

overall_design: Remnant bone fragments were collected intraoperatively by the staff of the Cooperative Human Tissue Network Eastern Division (CHTN-ED https://www.chtneast.org/). Samples were split for processing as frozen in liquid nitrogen vs. heat stabilization, followed by annotation and storage until the time of RNA extraction.

first: Samir

last: Mehta


title: Comparison of gene expression profiles of HCV-specific CD8 T cells from resolving and chronic patients.

status: Public on Jan 18 2017

first: David

last: Wolski

address: 55 Fruit Street

department: Gastrointestinal Unit

institute: Massachusetts General Hospital

summary:
T cell exhaustion is a well-defined process diminishing the efficacy of the CD8 response in persistent viremia. What is less understood is whether early differences in T cell regulation already predetermine the fate of the T cell response and infection outcome. Its dichotomous outcome  that is unique among human viral infections makes hepatitis C virus infection uniquely suited to compare transcriptional regulation between HCV-specific CD8 T cells that do and do not achieve viral control.
Using differential gene expression  and gene set enrichment analyses we validate HCV-specifcic CD8 T cell transcriptional modules.

overall_design: We sorted HCV-specific CD8 T cells from 3 resolving patients and 7 chronic patients at the earliest available time point during the acute phase of infection (≤21 weeks).

first: Georg

last: Lauer


title: Transcriptional response of human synovial fibroblasts to TNF and IL-17A (Microarray Data 2)

first: Hung

last: Nguyen

address: 1 Jimmy Fund Way, Smith Bldg 508

department: Rheumatology

institute: Brigham and Women's Hospital

summary: The combination of TNF and IL-17A has synergistic effects on the transcription of genes encoding chemokines and cytokines.

overall_design:
Human fibroblasts derived from 2 individuals with rheumatoid arthritis and 2 individuals with osteoarthritis were stimulated with TNF, IL-17A, or TNF and IL-17A and gene expression was assayed with microarrays.

Microarray Data 2 (n = 48): 1 time point (24 hours), 3 passages, 4 cell lines, 4 stimulations (Baseline; None; TNF; TNF and IL-17A).

GeneChip™ Human Genome U133 Plus 2.0 Array ("affy_hg_u133_plus_2" on Bioconductor).

first: Erika

middle: H

last: Noss

first: Christine

last: Huppertz

first: Gerald

last: Watts


title: 809094 Biomarker Identification in Fracture Healing (experiment #5200-5203 Jun 2015)

summary:
The specific genes that distinguish normal fracture healing from abnormal healing or nonunion in humans are unknown. This study was an exploratory investigation of peripheral blood from acutely injured fracture patients collected over multiple days to compare normal healers, slow healers, and nonunion outcomes.
We used microarrays to do a global comparison between acutely injured (AI) subjects (AIS) vs. age- and sex-matched healthy volunteers (HV) and chronic Nonunion (NU) patients.

overall_design: AIS and NU were enrolled into the study upon presentation for fracture care. Blood was collected into PaxGene blood RNA tubes during the inpatient stay and during clinical follow up. HV were enrolled in parallel with a one-time blood sample collection into PaxGene blood RNA tubes. RNA was extracted from all samples applicable to this experiment. We explored the data with Partek Genomics Suite using all samples at all time points to identify a panel of genes that is differentially expressed across groups to enable additional biomarker vetting.


title: Expression data for P. aeruginosa ATCC 33988 and P. aeruginosa PAO1 in Jet-A fuel

status: Public on Jan 10 2017

city: Dayton

first: thusitha

last: Gunasekera

state: OH

address: Firwood Drive

department: University of Dayton Research Institute

institute: University of Dayton

summary:
We investigated fuel specific transcriptomic differences between these strains in order to ascertain the underlying mechanisms utilized by the adapted strain P. aeruginosa ATCC 33988 to jet fuel to Jet-fuel
During growth in fuel, the genes related to alkane degradation, heat-shock response, membrane proteins, efflux pumps and several novel genes were upregulated in ATCC 33988

overall_design: Strain Comparison between strains

first: Thusitha


title: Classifying chemical endocrine activity using transcriptome profiling in zebrafish

city: Corvallis

first: Robert

last: Tanguay

state: OR

department: EMT

institute: Oregon State University

summary: We employed whole-genome microarray expression profiling in 48 hpf zebrafish as a tool to classify the activity of 25 endocrine disrupting chemicals

overall_design:
Chemical-induced transcriptional changes were measured in 48 hpf embryos exposed to vehicle control of the effective concentration where 80% of the exposed population has an adverse effect (EC80) from 6-48 hpf. Four biological replicates of 8 pooled whole embryos were used for each treatment
Please note that nine samples were removed from analysis due to outlier detection (resulting in 107 samples included in the records, out of total 116 samples).

first: Derik

last: Haggard


title: Effect of  low dose docosahexaenoic acid (DHA) on bovine cumulus cells during in vitro maturation

city: Nouzilly

first: Svetlana

last: UZBEKOVA

address: PRC INRA

country: France

institute: INRA

summary: In order to decipher the pathways of DHA via cumulus cells (CC) surrounding an oocytes,  microarray hybridization of cumulus cells after 4h IVM in the presence or absence of 1µM DHA was performed.

overall_design: Transcriptomes of cumulus cells from the oocytes after 4 hours of in vitro maturation (IVM) in the presence or absence of 1µM DHA were compared.

last: Uzbekova

first: Sebastien

last: Elis

first: Mouhamad

last: Oseikria

first: Anais

last: Vitorino Carvalho

first: Veronique

last: Duranthon


title: High-throughput sequencing and degradome analysis reveal differential expression of miRNAs and their targets between cytoplasmic male-sterile cybrid pummelo and its fertile type (Citrus grandis)

status: Public on Jan 09 2017

city: Wu Han

first: Yan-ni

last: Fang

address: shizi mountain street

institute: Huazhong Agricultural University

summary: High-throughput sRNA and degradome sequencing was applied in G1+HBP and its fertile type HBP to identify miRNAs and their targets during reproductive development. A total of 184 known miRNAs, 22 novel miRNAs and 86 target genes were identified. Some of the targets are transcription factors involved in floral development, such as auxin response factors (ARFs), SQUAMOSA promoter binding protein box (SBP-box), MYB, basic region-leucine zipper (bZIP), APETALA2 (AP2), transport inhibitor response 1 (TIR1), etc. Eight target genes were confirmed to be sliced by corresponding miRNAs using 5’RACE technology. Based on the sequencing abundance, 42 differentially expressed miRNAs between CMS line G1+HBP and fertile line HBP were discovered. Differential expression of miRNAs and their target genes was validated by quantitative RT-PCR and reciprocal expression patterns between some miRNAs and their targets were demonstrated. The regulation mechanism of miR167a was elucidated by yeast one-hybrid and dual-luciferase assay that a dehydrate responsive element binding (DREB) transcription factor bind miR167a promoter and transcriptionally repress miR167 expression. Our study revealed altered expression of miRNAs and their target genes in cytoplasmic male sterile pummelo (CMS) line and highlighted that miRNA regulatory network may be involved in nucleus-cytoplasmic cross talk of citrus CMS.

overall_design: small RNA and degradome sequencing of seedy ‘HBP’ and its cytoplasmic male sterile and seedless line ‘G1+HBP’

first: Yan-Ni

first: Bei-bei

last: Zheng

first: Lun

last: Wang

first: Xiao-Meng

last: Wu

first: Wen-Wu

last: Guo

first: Qiang

last: Xu


title: 809094 Biomarker Identification in Fracture Healing (experiment #5149 Feb 2015)

status: Public on Jan 06 2017

first: Annamarie

last: Horan

summary:
The specific genes that distinguish normal fracture healing from abnormal healing or nonunion in humans are unknown.  This study was an exploratory investigation of peripheral blood from  acutely injured fracture patients collected over multiple days to compare normal healers, slow healers, and nonunion outcomes.
We used microarrays to do a global comparison between acutely injured (AI) subjects (AIS) vs age and sex matched healthy volunteers (HV) and chronic Nonunion (NU) patients.

overall_design: AIS and NU were enrolled into the study upon presentation for fracture care.  Blood was collected into Paxgene blood RNA tubes during the inpatient stay and during clinical follow up.  HV were enrolled in parallel with a one-time blood sample collection into Paxgene blood RNA tubes. RNA was extracted from all samples applicable to this experiment.  We explored the data with Partek Genomics suite using all samples at all time points to identify a panel of genes that is differentially expressed across groups to enable additional biomaker vetting.

first: Samir

last: Mehta


title: 809094 Biomarker Identification in Fracture Healing (experiment #3808a mRNA)

overall_design: Remnant bone fragments were collected intraoperatively by the staff of the Cooperative Human Tissue Network Eastern Division (CHTN-ED https://www.chtneast.org/). Samples were split for processing as frozen in liquid nitrogen vs heat stabilization followed by annotation and storage until the time of RNA extraction.


title: 809094 Biomarker Identification in Fracture Healing (experiment #3873a mRNA performed Apr 2011)

summary:
The specific genes that distinguish normal fracture healing from abnormal healing or nonunion in humans are unknown.  This study was an exploratory investigation of peripheral blood from 2 chronic nonunion patients collected perioperatively (pre/post revision surgery) and at 3 months post revision follow up for comparison to Acutely injured subjects and Healthy volunteer cohorts analyzed separately.
We used microarrays to do a global comparison between 2 chronic nonunion patients collected perioperatively (pre/post revision surgery) and at 3 months post revision follow up.

overall_design: Blood was collected into Paxgene blood RNA tubes pre and post operatively during admission for revision surgery in 2 chronic nonunion patients.  Blood was collected again at 3 months follow up. We explored the data with Partek Genomics suite using all samples at all time points to identify a panel of genes that is differentially expressed across  groups to enable additional biomaker vetting.


title: 809094 Biomarker Identification in Fracture Healing (experiment #3873 miRNA performed Apr 2011)


title: 809094 Biomarker Identification in Fracture Healing (experiment #3341 performed 2010 Jun) [mRNA]

summary:
The specific genes that distinguish normal fracture healing from abnormal healing or nonunion in humans are unknown.  This study was an exploratory investigation of peripheral blood from acutely injured fracture patients for comparison to age and sex matched healthy volunteers.
We used microarrays to do a global comparison between acutely injured (AI) subjects (AIS) vs age and sex matched healthy volunteers (HV).

overall_design: AIS were enrolled into the study upon presentation for fracture care.  Blood was collected into Paxgene blood RNA tubes during the inpatient stay.  HV were enrolled in parallel with a one-time blood sample colleciton into Paxgene blood RNA tubes. RNA was extracted from all samples applicable to this experiment.  We explored the data with Partek Genomics suite using all samples at all time points to identify a panel of genes that is differentially expressed across the two groups to enable additional biomaker vetting.


title: The microbial taxonomic and functional compositions in three broadleaved forests in temperate and subtropical zones

city: Beijing

first: yang

last: sihang

address: Haidian district Shuangqing road #30

institute: Tsinghua University

summary: Global warming has shifted climate zones poleward or upward. However, understanding the responses and mechanism of microbial community structure and functions relevant to natural climate zone succession is challenged by the high complexity of microbial communities. Here, we examined soil microbial community in three broadleaved forests located in the Wulu Mountain (WLM, temperate climate), Funiu Mountain (FNM, at the border of temperate and subtropical climate zones), or Shennongjia Mountain (SNJ, subtropical climate).Soils were characterized for geochemistry, Illumina sequencing was used to determine microbial taxonomic communities and GeoChips 5.0 were used to determine microbial  functional genes.

platform_organism: Bacteria Archaea Eukaryota

overall_design: Thirty samples were collected from three mountains in temperate and subtropical zones, with 10 replicates in every site

first: Sihang

last: Yang

first: Yuguang

last: Zhang

first: Yunfeng


title: In silico gene expression profiling of Cannabis sativa

status: Public on Jan 13 2017

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

country: Italy

institute: Ospedale San Raffaele

summary: Even if a large amount of high-throughput functional genomic data exists, most researchers feature a strong background in molecular biology but lack advanced bioinformatics skills. In this work, publicly available gene expression datasets have been analyzed giving rise to a total of 40,224 gene expression profiles within different Cannabis tissues/developmental stages. The resource here proposed will provide researchers with a starting point for future investigations of Cannabis sativa.

overall_design:
Thirty-one publicly available RNA-seq datasets have been re-analyzed from BioProject PRJNA80055 (SRA Study SRP006678) and BioProject PRJNA73819 (SRA Study SRP008673).
Details of the 31 re-analyzed samples and data processing can be found in Readme.txt.
Re-analysis results can be found in Gene_expression_counts.txt.


title: Comparison of gene expression profiles of HCV-specific CD8 T cells from resolving patients and HCV-specific CD8 T cells chronic patients that target conserved or escaped epitopes.

first: David

last: Wolski

state: MA

summary:
T cell exhaustion is a well-defined process diminishing the efficacy of the CD8 response in persistent viremia. What is less understood is whether early differences in T cell regulation already predetermine the fate of the T cell response and infection outcome. Its dichotomous outcome  that is unique among human viral infections makes hepatitis C virus infection uniquely suited to compare transcriptional regulation between HCV-specific CD8 T cells that do and do not achieve viral control.
Using differential gene expression analysis and gene co-expression networks we define core programs of T cell regulation but also extensive differences in metabolic and nucleosomal processes as well as their underlying regulation by transcription factors.

overall_design: We sorted HCV-specific CD8 T cells from 21 resolving patients and 22 chronic patients (15 with cells targeting preserved and 7 with cells targeting escaped epitopes) at multiple time points during the acute phase of infection (≤36 weeks).

first: Georg

last: Lauer


title: 809094 Biomarker Identification in Fracture Healing (experiment #3303 performed 2010 Mar)

status: Public on Jan 05 2017

summary:
The specific genes that distinguish normal fracture healing from abnormal healing or nonunion in humans are unknown.  This study was an exploratory investigation of peripheral blood from  acutely injured fracture patients collected over multiple days compared to age and sex matched healthy volunteers.
We used microarrays to do a global comparison between acutely injured (AI) subjects (AIS) vs age and sex matched healthy volunteers (HV).

overall_design: AIS were enrolled into the study upon presentation for fracture care.  Blood was collected into Paxgene blood RNA tubes daily during the inpatient stay.  HV were enrolled in parallel with a one-time blood sample colleciton into Paxgene blood RNA tubes. RNA was extracted from all samples applicable to this experiment.  We explored the data with Partek Genomics suite using all samples at all time points to identify a panel of genes that is differentially expressed across the two groups to enable additional biomaker vetting.


title: Transcriptional profiling by next generation sequencing of the spleen and splenic macrophages in the hamster model of visceral leishmaniasis

city: Galveston

first: Peter

last: Melby

state: TX

address: Marvin Graves Bldg, Rm. 4.210, Route 0435

department: Department of Microbiology and Immunology

institute: University of Texas Medical Branch

summary: We used next generation sequencing to examine global changes in gene expression in the spleen and splenic macrophages in a hamster model of progressive visceral leishmaniasis. We used RNA sequencing coupled with de novo transcriptome assembly, because the Syrian hamster does not have a fully sequenced and annotated reference genome. Libraries for deep sequencing were constructed from poly-A RNA isolated from the spleens or splenic macrophages of uninfected and 28-day L. donovani-infected hamsters (n=4 per group) using standard Illumina protocols. The library quality was confirmed by Agilent Bioanalyzer. Paired-end 50-base sequencing was performed using TruSeq SBS kit v3 (Illumina) on an Illumina HiSeq 1000.The quality of raw sequencing reads was checked using FastQC (v0.10.1). To avoid the contamination of pathogen sequences, we filtered out reads (using the FASTX Toolkit v0.0.13) that aligned to the Leishmania donovani BPK282A1 genome (NCBI BioProject PRJEA61817) using Bowtie 2 (v2.0.0-beta5) under default options. To reduce the effect of low quality reads, we further filtered out artifacts and reads having a phred score <28 in more than 10% of nucleotides using FASTX Toolkit (v0.0.13). Both forward and reverse reads were removed if any of them failed to pass the filters. To obtain a complete transcriptome, we used two steps. First, the cleaned sequencing reads from different spleen samples were pooled together and de novo assembled using Trinity software. Second, the resulting transcriptome was combined with all cleaned reads from hamster spleen and splenic macrophages and the CHO-K1 RefSeq genome to perform a second de novo assembly using BRANCH. We first created a customized reference library using Rattus norvegicus (Rnor_5.0.73) and Mus musculus (GRCm38.73) genomes. We then used BLAST (v 2.2.28+) to align each transcript generated from BRANCH against the customized library to assign it a gene name based upon sequence similarity. An E-value cutoff of <1e-3 was used. Additionally, we compared the Trinity transcripts with the CHO-K1 Ref Seq genome. All the non-Leishmania-like raw sequencing reads were first mapped to our de novo reference genome using Bowtie2 (v2.1.0) with default options, but allowing one read to map to as many as 500 different transcripts. We then measured the expression abundance, count of reads mapped to each transcript, using the software eXpress. To identify differentially expressed transcripts in each experiment, 3 different approaches were applied: exact tests of Robinson and Smyth and generalized linear models with the likelihood ratio test using the BioConductor R package EdgeR, and the Wald test using DESeq2. Only transcripts with at least 1 count per million in at least 3 out of 4 samples in the control or experimental group were included in the analysis. A transcript was considered differentially expressed only when it was identified by all three different approaches. Analysis of differentially expressed transcripts identified a highly inflammatory spleen environment with abundant expression of type I and type II interferon response genes. However, high IFN-γ expression was ineffective in directing exclusive M1 macrophage polarization, suppressing M2-associated gene expression, and restraining parasite replication and disease. While many IFN-inducible transcripts were upregulated in the infected spleen, fewer were induced in splenic macrophages in VL suggesting suppression of macrophage responsiveness to activating cytokines. The transcription factor STAT3 was predicted and confirmed to be activated, and found to orchestrate an exuberant counter-regulatory response that favors parasite replication.

overall_design: Transcriptional profiles of 28-day Leishmania donovani infected Syrian outbred hamsters were generated by deep sequencing, in quadruplicate, using Illumina  Illumina HiSeq 1000

first: Fanping

last: Kong

first: Omar

last: Saldarriaga

first: Heidi

last: Spratt

first: Bruce

last: Luxon


title: 809094 Biomarker Identification in Fracture Healing (experiment #4068 performed)

summary:
The specific genes that distinguish normal fracture healing from abnormal healing or nonunion in humans are unknown. This study was an exploratory investigation of peripheral blood from acutely injured fracture patients collected over multiple days compared to age- and sex-matched healthy volunteers. Bone fragments were collected from acutely injured subjects during surgery through the Cooperative Human Tissue Network-Eastern Division (CHTN-ED http://pathology.med.upenn.edu/research/centers-and-institutes/cooperative-human-tissue-network).
We used microarrays to do a global comparison between acutely injured (AI) subjects (AIS) and chronic Nonunion (NU) subjects vs. age- and sex-matched healthy volunteers (HV). We also compared tissue types by capturing bone fragments from the fracture site where possible.

overall_design: AIS and NU were enrolled into the study upon presentation for fracture care. Blood was collected into PaxGene blood RNA tubes daily during the inpatient stay. HV were enrolled in parallel with a one-time blood sample collection into PaxGene blood RNA tubes. RNA was extracted from all samples applicable to this experiment. Bone fragments were collected through the CHTN-ED from eligible cases. We explored the data with Partek Genomics Suite using all samples at all time points to identify a panel of genes that is differentially expressed across the two groups to enable additional biomarker vetting.


title: Expression data from Rspo1-null differentiating primary myoblasts

status: Public on Jan 01 2017

city: Lyon

first: Fabien

last: Le Grand

address: 8 avenue Rockefeller

department: Melis

institute: Institut Neuromyogene

summary:
Regeneration of the adult skeletal muscle tissue relies on a population of muscle stem cells called satellite cells. During tisse repair, satellite cells exhibit active canonical Wnt/beta-catenin signaling. Rspo1 is a modulator of Wnt signaling in many tissue, and is expressed by muscle progenitor cells.
To identify genes that become transcribed following activation of the Wnt/β-Catenin pathway in satellite cells, we performed microarray analysis of primary myoblasts expressing an active form of beta-catenin

overall_design: Primary myoblasts were prepared from the limb muscles of wild-type and Rpos1-null mice. RNA was extracted from two independent cultures for each conditions.

first: Floriane

last: Lacour


title: 809094 Biomarker Identification in Fracture Healing (experiment #5201-5202 Jun 2015)


title: Calcium effect to the Clostridium beijerinckii NCIMB 8052 degenerate strain for the solvent producing recovery

status: Public on Jan 02 2017

city: Xi'an

first: Bei

last: Han

state: Shaanxi

address: NO 76 Yanta West Road

department: School of Public Health

institute: Xi'an Jiaotong University

summary: Solventogenic Clostridium species ferment carbohydrates to acetone, butanol and ethanol which are well-known next-generation biofuels. However, repeated subculture of or continuous fermentation by Clostridium often decreases and eventually terminates the solvent production and spore formation, which is a process called strain degeneration. Supplementation of CaCO3 to fermentation medium could partially recover metabolism of degenerated strain by more than 50% increase of cell growth and solvent production. The transcriptome profile of Clostridium beijerinckii NCIMB 8052 (DG-8052) and its response to CaCO3 treatment were analysed by microarray. Since fermentation by C. beijerinckii NCIMB 8052 is a biphasic process, gene expressions of two fermentations were compared at each stage, i.e. 12h and 24h fermentation time representing acidogenic phase and solventogenic phase, respectively. This study examined expression of 5168 genes capturing 98.6% of the C. beijerinckii NCIMB 8052 genome. With the addition of CaCO3, DG-8052 had 565 and 916 genes significantly up-regulated at acidogenic phase and solventogenic phase, respectively. According to the enrichment analysis of pathway and Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, these genes were significantly overrepresented in cellular functions such as Amino acid transport and metabolism, organic acid biosynthetic process, bacteria chemotaxis and defense mechanisms. On the other hand, there were 704 and 1044 genes significantly down-regulated at acidogenic phase and solventogenic phase, respectively. These repressed genes were mainly enriched in functions such as ion transmembrane transport, ATP synthesis, oxidative phosphorylation.

overall_design:
Clostridium beijerinckii NCIMB8052 degenerated strain cells in P2 medium vs. Clostridium beijerinckii NCIMB8052 degenerated strain cells in P2 medium with 4g/L CaCO3
Two-fermentation time points (12h and 24h) experiments (degenerated strain cells in P2 vs.degenerated strain cells in P2 with CaCO3);Biological replicates: 3 replicates of degenerated strain cells in P2 at 12h; 3 replicates of degenerated strain cells in P2 at 24h;3 replicates of degenerated cells in P2 with CaCO3 at 12h;3 replicates of degenerated cells with CaCO3 at 24h.

first: Yan


title: Mutational blows to Sox2+ cells induce epithelial squamous tumor initiation

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

summary: Cancer originates as the progressive accumulation of genetic mutations in proto-oncogenes and tumor suppressors. However, the early events underlying tumor initiation remain largely elusive, mostly due to the general lack of information regarding the cells-of-origin responsible for tumor formation as well as the precise impacts of genetic insults on tumor initiation in vivo. Here, we demonstrate that Sox2-positive (Sox2+) adult stem cells are responsible for epithelial squamous tumor formation. Conditional expression of oncogenic Kras (KrasG12D) and knockout of p53 (also known as Trp53) in Sox2+ cells quickly and specifically resulted in the formation of squamous tumors in the forestomach and esophagus. GFP-based lineage tracing experiments demonstrated that Sox2+ cells are the cells-of-origin of squamous tumors in the esophagus and forestomach. Of note, our data showed that p53 deletion alone did not suffice for tumor initiation. On the contrary, tumor initiation was observed upon KrasG12D activation whereas p53 deletion further contributed to the malignancy of the generated tumors, pointing out distinct roles for Kras activation and p53 deletion in squamous tumor formation and progression, to which a multihit carcinogenesis model can be applied. Global gene expression analysis revealed secreting factors upregulated in the generated tumors induced by oncogenic Kras, which contribute to tumor progression. Taken together, these results demonstrate that epithelial squamous tumors can specifically originate as a consequence of defined genetic mutations in a Sox2+ cell population and highlight the connections between proliferative stem cells and tumor development in vivo.

overall_design: Expression profiling of mouse tissues with genetically induced tumors by RNA-Seq

first: Tomoaki

last: Hishida

first: Juan

last: Belmonte


title: 809094 Biomarker Identification in Fracture Healing (experiment #3218 performed 2009 Nov)

status: Public on Jan 04 2017

first: Annamarie

last: Horan

summary:
The specific miRNAs that distinguish normal fracture healing from abnormal healing or nonunion in humans are unknown.  This study was an exploratory investigation of peripheral blood from 2 acutely injured fracture patients collected over multiple days compared to age and sex matched healthy volunteers.
We used microarrays to do a global comparison between acutely injured (AI) subjects (AIS) vs age and sex matched healthy volunteers (HV).

first: Samir

last: Mehta


title: Gene expression in limited cutaneous systemic sclerosis skin

city: Lebanon

first: Tammara

last: Wood

state: NH

address: WTRB 674

department: Biomedical Data Science

institute: Dartmouth Medical School

summary: Systemic sclerosis (SSc) is an autoimmune disease characterized by clinical heterogeneity, multi-organ involvement, and complex genetic risk. Here, we report the first multi-tissue meta-analysis of ten independent SSc gene expression datasets. We identify a common immune-fibrotic expression axis across all tissues that is associated with the most severe disease phenotypes. The coexpression patterns conserved across tissues and phenotypes were used to query functional genomic networks, which allowed us to identify common and tissue-specific disease drivers. We find evidence of pro-fibrotic macrophages (MØs) in SSc end-target organs. Prominent genes in the skin functional genomic network are associated with SSc genetic risk and are modulated by immunosuppressive treatment in clinical improvers. These data suggest the interactions between T lymphocytes and MØs are a critical driver of disease and implicate MØs as central to SSc pathogenesis. In total, this study presents a mechanism for fibrosis in SSc end-target tissues, a set of putative therapeutic targets for modulating SSc, and a framework for multi-tissue functional genomic studies of complex human disease.

overall_design: Gene expression was measured in forearm skin punch biopsies in 24 limited cutaneous systemic sclerosis patients

first: Robert

last: Lafyatis

first: Michael

last: Whitfield


title: DNA methylation profiling of nenonatal murine hearts

status: Public on Dec 31 2016

city: Gdansk

first: Pawel

last: Sachadyn

address: Narutowicza 11/12

department: Molecular Biotechnology and Microbiology

institute: Gdansk University of Technology

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

overall_design: genome-wide DNA methylation profiling in the hearts of C57BL/6J mouse

first: Paweł


title: A systems approach reveals MAVS signaling in myeloid cells as critical in resistance to Ebola virus in murine models of infection

city: New York

first: Angela

last: Rasmussen

department: Center for Infection and Immunity

institute: Columbia University

summary: The unprecedented 2013-16 outbreak of Ebola virus (EBOV) in West Africa resulted in over 11,300 human deaths. Host resistance to EBOV is thought to involve RIG-I-like receptor (RLR) signaling through the adaptor protein, mitochondrial antiviral signaling (MAVS), but role of RLR-MAVS in orchestrating anti-EBOV responses in vivo is not known. Here, we apply a systems approach to MAVS-deficient mice infected with either wild-type or mouse-adapted EBOV. MAVS controlled EBOV replication through expression of IFNα, IFN-stimulated genes, and regulation of inflammatory responses in the spleen, and prevented cell death in the liver, with macrophages implicated as a major cell-type influencing host resistance. A dominant role for RLR signaling in macrophages was confirmed following conditional deletion of MAVS in LysM+ myeloid cells. These findings reveal tissue-specific transcriptional pathways controlled by RLR signaling in resistance to EBOV, and suggest that EBOV adaptation to cause disease in mice is linked in part to increased antagonism of RLR-dependent signaling.

overall_design: RNA was isolated from the liver and spleen of mice (C57BL/6 or MAVS-/-) that were either mock-infected or infected with mouse-adapted Ebola virus (MA-EBOV). These were run on Agilent microarrays to assess differences in gene expression related to MAVS signaling during the course of MA-EBOV infection.

first: Sonja

last: Best

first: Mukta

last: Dutta

last: Katze


title: ZCF32, a fungus specific Zn(II)2-Cys6 transcription factor, is a major regulator of the biofilm circuit in the human pathogen Candida albicans

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

summary: To delineate the functional role of ZCF32 in Candida albicans biology, we carried out the genome wide expression analysis of wild-type and zcf32 null mutants by global expression array. We analysed the gene expression profiles of YPK102/1 and YPK102/2 and the parent wild type (SC5314) strain grown in YPD liquid medium at 30°C till the start of the stationary phase.  In the microarray analysis, a total of 607 genes were found to be differentially expressed  (fold change < 1.5 at p-value < 0.05) between the wild type and two zcf32 null mutants. Out of the 607 differentially expressed genes, 438 genes were up-regulated whereas 169 genes were down-regulated. Gene ontology (GO) analysis of up-regulated and down-regulated genes suggests that biofilm, filamentation, iron homeostasis, cell wall biogenesis, oxidation, and cell cycle are the major pathways altered in zcf32 null mutant.

overall_design: Organism : Candida albicans , Agilent Custom Candida albicans Gene Expression  8x15k Array (AMADID: 026377) designed  by Genotypic Technology Private Limited.

first: Pallavi

last: Kakade

first: V

last: Nagaraja

first: Kaustuv

last: Sanyal