title: Hedgehog gradient in the stroma maintains niche diversity and organ function [Drop-seq]

first: Peng

last: Tien

address: 513 Parnassus Ave, Health Sciences East 1350

department: Department of Pulmonary Medicine

institute: University of California San Francisco

summary: A single-cell transcriptional analysis was performed on GLI2+ stromal cells from the adult murine lung. Whole adult murine lung tissue was dissociated to single cells and subjected to fluorescence activated cell sorting (FACS) to select all live GLI2+ cells. The single cell RNA-sequencing library was then subsequently generated. Cells were sequenced at a depth of ~60,000 reads/cell. We captured approximately 4,600 cells with a median of 2,246 genes detected per cell utilizing a droplet-based barcoding approach to capture single cells for RNA sequencing. The results demonstrate that the GLI2+ population is segregated into distinct stromal subtypes along the proximal-distal axis of the lung with distinct functional contribution to matrix production and paracrine signaling within their distinctive niche.

overall_design: The CreERT2-2A-tdTomato expression cassette was inserted into the Gli2 locus to generate a murine tool that allows us to isolate GLI2+ cells by endogenous tdTomato reporter expression. Whole adult murine lung tissue was dissociated to single cells, stained with anti-CD45-PE-Cy7, anti-Epcam-BV421 and DAP, and subjected to FACS to select live GLI2+ cells. Doublets and dead cells were excluded based on forward scatter, side scatter and DAPI fluorescence. The hematopoietic cells were excluded by stained with anti-CD45-PE-Cy7 and the epithelial cells were excluded by stained with Epcam-BV421. Then the GLI2+ cells were sorted by endogenous tdTomato fluorescence. The live GLI2+ cells were prepared using the 10X single cell instrument and v1 10X single cell kits according to standard protocol. Single cell sequencing of adult murine lung GLI2+ population was performed by using the HiSeq2500.

first: Chaoqun

last: Wang

first: Tien

last: Peng


title: Duodenal adenoma/adenocarcinomas vs matched normal mucosa

status: Public on Aug 06 2018

city: Tokyo

first: Nobutake

last: Yamamichi

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Gastroenterology, Graduate School of Medicine

country: Japan

institute: The University of Tokyo

summary:
Background: Duodenal adenoma/adenocarcinomas are rare, and the global gene expression changes associated with the initial stages of carcinogenesis of these neoplasms have not been elucidated. Results: To comprehensively analyze genetic markers and pathways specific to early-stage duodenal adenoma/adenocarcinomas, transcriptional profiles of 4 fresh-frozen non-ampullary duodenal adenoma/adenocarcinomas and surrounding duodenal normal mucosa were compared. Key features of gene expression analysis demonstrated a strong correlation between these tumors and colorectal adenomas, as well as the Wnt/β-catenin pathway. These results shed new light on the transcriptional changes that occur during the early stages of duodenal tumorigenesis.
All samples were obtained prior to treatment in order to minimize effects of cauterization, and immediately fresh-frozen.

overall_design: Biopsy samples from duodenal adenoma/adenocarcinomas and corresponding normal mucosa were obtained during endoscopy. The tissues were collected prospectively with informed consent and the approval of the institutional review board.

first: Yoshiki

last: Sakaguchi

first: Shuta

last: Tomida


title: Genome wide mapping of Npa1-HTP binding sites in yeast by CRAC

status: Public on Aug 07 2018

city: PARIS

first: Simon

last: Lebaron

address: 4 avenue de l'observatoire

country: France

institute: Université Paris Descartes

summary: We report the application of the Cross-Linking and cDNA (CRAC) technique to identify binding sites of Npa1, ribosome assembly factors, on RNAs in vivo.

overall_design: We compare sequences enrichement of RNAs associated to Nap1_HTP or to a mock (un-tagged) control after protein/RNA cross-link in vivo.

first: Anthony

middle: K

last: Henras


title: Genome-wide H3K27ac profiles in post-mortem entorhinal cortex samples from Alzheimer's disease cases and controls

status: Public on Aug 11 2018

city: London

first: Sarah

last: Marzi

address: DeCrespigny Park

department: Institute of Psychiatry, Psychology and Neuroscience

country: United Kingdom

institute: King's College London

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We quantified genome-wide levels of H3K27ac in post-mortem entorhinal cortex tissue samples, identifying widespread Alzheimer's disease (AD)-associated acetylomic variation. Differentially acetylated peaks were identified in the vicinity genes implicated in both tau and amyloid neuropathology (MAPT, APP, PSEN1, PSEN2), as well as genomic regions containing variants associated with sporadic late-onset AD (CR1, TOMM40). Both MAPT and PSEN2 are characterized by an extended hyperacetylated region upstream of the TSS  mapping to enhancers in the brain. We show that genes annotated to AD-associated hyper- and hypoacetylated peaks are enriched for brain- and neuropathology-related  functions.

overall_design: Examination of variable H3K27ac across 47 individuals using ChIP-seq

first: Jonathan

last: Mill


title: CDK6 antagonizes p53-induced responses during tumorigenesis

city: Vienna

first: Markus

last: Zojer

address: Josef-Baumanngasse

department: Institute for Pharmakology and Toxokology

country: Austria

institute: University of Veterinary Medicine

type: Expression profiling by high throughput sequencing

summary: CDK6 induces a complex transcriptional program to block p53 in hematopoietic cells.  CDK6 binds to the promoters of genes including p53-antagonists. Cells lacking CDK6 kinase function are required to mutate p53 to achieve a fully transformed immortalized state.

overall_design: RNA Seq experiments were performed in two individually derived cell lines for each genotype. ChIP-Seq experiments were done in biological triplicates. Two individual input and three chromatin-immunoprecipitated fractions were sequenced. Cdk6-/- cell lines served as control.

first: Florian

last: Bellutti

first: Anca-Sarmiza

last: Tigan

first: Sofie

last: Nebenfuehr

first: Reinhard

last: Grausenburger

first: Veronika

last: Sexl


title: Hedgehog gradient in the stroma maintains niche diversity and organ function

status: Public on Aug 08 2018

city: San Francisco

state: CA

country: USA

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Gene expression changes in human K562 cells by a synthetic transcription factor (peptide), that mimics the Homeobox protein DLX4 or its isoforms, DLX7 or BP1.

status: Public on Aug 10 2018

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: Homeobox proteins are known as master regulators of developmental morphogenesis. DLX genes encode transcription factors that significantly regulate the hematopoitic system. DLX4 and its isoform BP1 are expressed in different stages of development in human hematopoitic cells and regulate further differentiation. BP1 is the repressor of adult beta and delta globin genes found in fetal and embryonic tissues and rarely observed in adult tissues. In K562, a human chronic myelogenous leukemia cell line, BP1 is found to be over-expressed.  In this study we have designed and synthesized a peptide-based artificial transcription factor that mimics the DNA binding domain of DLX4 homeodomain and can antagonise its binding. For the micro-array analysis we have taken peptide treated K562 cells and as control untreated K562 cells. Our study provides gene expression profile upon treatment of the homeodomain mimic.

overall_design: Organism : Homo sapiens, Agilent's Human Gene Expression  8x60k Array (AMADID: 039494)

first: Basusree

last: Ghosh

first: Siddhartha

last: Roy


title: Gene expression data from posterior fossa ependymomas

status: Public on Aug 03 2018

city: Memphis

first: ji

last: wen

state: Tennessee

address: 262 Danny Thomas Place

department: pathology

institute: st jude children's research hospital

summary: We have discovered two major molecular subgroups of PFA molecular group posterior fossa ependymomas by DNA methylation profiling. These are also distinguished by gene expression profiling using Affymetrix U133v2 arrays with correspondence to data generated by DNA methylation profiling.

overall_design: Total RNA from 39 ependymal tumor samples were hybridised to the Affymetrix HG U133 Plus 2.0 microarrays.

first: Ji

last: Wen

first: Ruth

middle: G

last: Tatevossian

first: Wilda

last: Orisme

first: Bo

last: Tang

first: Chandanamali

last: Punchihewa

first: Ryan

middle: P

last: Lee

first: David

middle: W

last: Ellison

first: Kristian

last: Pajtler

first: Martin

last: Sill

first: Marcel

last: Kool


title: Hierarchical control of the IL-13 signals by STAT6 and SOX11 in lung fibroblasts

status: Public on Aug 02 2018

city: Saga

first: Satoshi

last: Nunomura

address: 5-1-1 Nabeshima

department: Department of Biomolecular Sciences

institute: Saga Medical School


title: Architectural proteins and pluripotency factors cooperate to orchestrate the transcriptional response of hESCs to temperature stress

city: XIAMEN

first: XIAOWEN

last: LYU

state: FUJIAN

address: No.4221, Xiang'an South Road, Xiang'an District

country: China

institute: XIAMEN UNIVERSITY

summary: Cells respond to temperature stress via up- and down-regulation of hundreds of genes. This process is regulated by the heat shock factor HSF1, which controls the release of RNAPII from promoter-proximal pausing. Here we analyze the events taking place upstream of transcription elongation in hESCs. We find that temperature stress results in the activation or decommissioning of thousands of enhancers. This process involves alterations in the occupancy of transcription factors HSF1, AP-1, NANOG, KLF4, and OCT4, which is accompanied by changes in H3K27ac and H3K27me3, as well as nucleosome remodeling by BRG1. In addition, redistribution of RAD21 and CTCF results in the formation and disassembly of interactions mediated by these two proteins, either individually or in combination. These alterations either tether/untether enhancers to their cognate promoters or remodel insulated neighborhoods with the ultimate goal of transforming the landscape of enhancer-promoter interactions. This loop remodeling process supports unidirectional loop extrusion as a mechanism for the establishment of CTCF/cohesin loops.

overall_design: Hi-C, HiChIP, ChIP-seq, ATAC-seq, eU-Seq

first: Xiaowen

last: Lyu

first: Jordan

last: Rowley

first: Victor

last: Corces


title: Hierarchical control of the IL-13 signals by STAT6 and SOX11 in lung fibroblasts (NHLF cells)

summary: We sought to dissect SOX11-dependent and -independent genes in IL-13–inducible genes in primary human lung fibroblasts

overall_design: Normal human primary lung fibroblasts (NHLF) were treated with SOX11 siRNA or control siRNA and then cultured for 24 hours in the presece or absence of IL-13. A single experiment was performed.

first: Kenji

last: Izuhara

first: Yasutaka

last: Mitamura


title: Genome-wide analysis of coding, long noncoding RNA and miRNA expression for NHLF after treatment with 10 ng/ml of IL-13

city: Los Angeles

first: Masafumi

last: Horie

address: 2011 Zonal Ave

institute: University of Southern California

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

platform_organism:
Homo sapiens
synthetic construct


title: miRNA expression profile for NHLF after treatment with 10 ng/ml of IL-13

summary: To assess miRNA expression by IL-13 in NHLF, we carried out a miRNA analysis of NHLF treated with  a with 10 ng/ml of IL-13 on 4 and 24 hr. We used the GeneChip® miRNA 4.0 Array

overall_design: NHLF were treated with 10 ng/ml of IL-13 on 1, 4, and 24 hr.

first: Hideyuki

last: Takeshima


title: Genome-wide analysis of gene expression for NHLF after treatment with 10 ng/ml of IL-13

summary: Normal human lung fibroblasts were stimulated by IL-13, and global gene expression profile was assessed by cDNA microarray

overall_design:
For gene expression profiling, total RNA was extracted from NHLFs at 0, 1, 4, and 24 h after IL-13 stimulation using the miRNeasy Mini kit (Qiagen).
Microarray analysis was performed using Agilent SurePrint G3 Human Gene Expression 8x60K v3 (Agilent Technologies, Wilmington, DE, USA).


title: Circulating miRNome profiling in Moyamoya disease-discordant monozygotic twins and endothelial microRNA expression analysis using iPS cell line

city: Sapporo

first: Masaki

last: Ito

address: North 15 West 7

department: Neurosurgery

institute: Hokkaido University

summary: We aim to investigate circulating genome-wide microRNA (miRome) profiles in Moyamoya disease (MMD)-discordant monozygotic (MZ) twins with the RNF213 founder mutation (rs112735431).A disease discordant monozygotic twin-based study design may unmask potential confounders from previously published circulating microRNA signature in MMD. Circulating genome-wide microRNA (miRNome) profiling was performed in MMD-discordant monozygotic twins, non-twin-MMD patients, and non-MMD healthy volunteers by microarray followed by qPCRvalidation, using blood samples. Differential plasma-microRNAs were further quantified in endothelial cells differentiated from iPS cell lines (iPSECs) derived from another independent non-twin cohort. Lastly, their target gene expression in the iPSECs was analyzed. Microarray detected 309 plasma-microRNAs in MMD-discordant monozygotic twins that were also detected in the non-twin cohort. Principal component analysis of the plasma-microRNA expression level demonstrated distinct 2 groups separated by MMD and healthy control in the twin- and non-twin cohorts. Of these, differential up-regulations of hsa-miR-6722-3p/-328-3p were validated in the plasma of MMD (Imposed threshold: absolute log2 expression fold change (logFC) > 0.26 for the twin cohort; absolute logFC > 0.26, p < 0.05, and q < 0.15 for the non-twin cohort). In MMD derived iPSECs, hsa-miR-6722-3p/-328-3p showed a trend of up-regulation with a 3.0- or higher expression fold change. Bioinformatics analysis revealed that 41 target genes of miR- 6722-3p/-328-3p were significantly down-regulated in MMD derived iPSECs and were involved in STAT3, IGF-1-, and PTEN-signaling, suggesting a potential microRNA- gene expression interaction between circulating plasma and endothelial cells. In conclusion, our MMD-discordant monozygotic twin-based study confirmed a novel circulating microRNA signature in MMD as a potential diagnostic biomarker minimally confounded by genetic heterogeneity. The novel circulating microRNA signature can contribute for the future functional microRNA analysis to find new diagnostic and therapeutic target of MMD.

overall_design: A pair of disease discordant twins (n=2), unrelated MMD cases (n=9) and normal healthy controls (n=10)

first: Haruto

last: Uchino

first: Ken

last: Kazumata

first: Yuka

last: Hama

first: Shuji

last: Hamauchi

first: Hidenao

last: Sasaki

first: Kiyohiro

last: Houkin


title: A Chemical Kinetic Basis for Measuring Translation Initiation and Elongation Rates from Ribosome Profiling data

city: University Park

first: Nabeel

last: Ahmed

state: PENNSYLVANIA

address: 407 Chemistry Building

department: The Huck Institutes of the Life Sciences

institute: Pennsylvania State University

summary: Analysis methods based on simulations and optimization have been previously developed to estimate relative translation rates from next-generation sequencing data. Translation involves molecules and chemical reactions; hence, bioinformatics methods consistent with the laws of chemistry and physics are more likely to produce accurate results. Here, we derive simple equations based on chemical kinetic principles to measure the translation-initiation rate, transcriptome-wide elongation rate, and individual codon translation rates from ribosome profiling experiments. Our methods reproduce the known rates from ribosome profiles generated from detailed simulations of translation. Applying our methods to data from S. cerevisiae and mouse embryonic stem cells we find that the extracted rates reproduce previously reported correlations with various molecular quantities. A codon can exhibit up to 26-fold variability in its translation rate depending upon its context with in a transcript. This broad distribution means that the average translation rate of a codon is not representative of the rate at which most instances of that codon are translated. We also find that mouse embryonic stem cells have a global translation speed that is almost two-fold faster than previously reported. This large variability in translation rates suggests that translational regulation might be used by cells to a greater degree than previously thought.

overall_design: RNA-Seq data corresponding to Ribosome profiling data (GSE75322) of two biological replicates of S288C yeast cells

first: Ulrike

middle: A

last: Friedrich

first: Ajeet

last: Sharma

first: Pietro

last: Sormanni

first: Guenter

last: Kramer

first: Edward

last: O'Brien


title: Host-directed adjunctive therapy with pravastatin against chronic TB in mice

city: Baltimore

first: Noton

last: Dutta

state: MD

address: 1550 Orleans Street, Room 110

department: Medicine

institute: Johns Hopkins University

summary:
Mycobacterium tuberculosis (Mtb) is known to subvert immune responses to establish infection and cause disease. Thus, host-directed therapy (HDT), as adjunctive treatment to traditional antitubercular regimens, is an attractive strategy. Statins are a class of drugs used to lower cholesterol levels by inhibiting the 3-hydroxy-3-methylglutaryl coenzyme A reductase, a crucial enzyme in the cholesterol biosynthesis pathway. Here, we conducted a preclinical animal study aimed at comparing the bactericidal activities of the standard TB regimen (rifampin, isoniazid, pyrazinamide and ethambutol; RHZE) with or without escalating doses of pravastatin against chronic TB in BALB/c mice. Antibiotics were given five times weekly for 8 weeks (continuous phase) beginning 6 weeks after infection. Treatment with RHZE plus pravastatin at doses ranging from 30 mg/kg to 180 mg/kg demonstrated a dose-dependent increase in bactericidal activity, reducing lung bacillary counts by 0.2–0.6 log10, 0.3–0.6 log10 and 0.3–0.8 log10 compared to RHZE alone at weeks 2, 4 and 8, respectively. After 8 weeks of treatment, the degree of lung inflammation correlated with the bactericidal activity of each drug regimen.
In order to gain insight into the anti-TB mechanism of action of pravastatin in vivo, the lungs of mice treated with pravastatin adjunctive therapy and those treated with RHZE alone were analyzed by whole-genome microarrays and RT-PCR. Mouse sera were studied by multiplex enzyme-linked immunosorbent assays. Treatment with pravastatin for 1 month had a profound effect on the global transcription in mouse lungs.

overall_design: Mtb-infected BALB/c mice were treated with the standard TB regimen (RHZE= rifampicin 10 mg/kg+ isoniazid 10 mg/kg + pyrazinamide 150 mg/kg+ ethambutol 100 mg/kg) with or without increasing doses of pravastatin (30, 90, 180 mg/kg). Treatment was given orally five times weekly for 4 weeks (continuous phase) beginning 6 weeks after infection

first: Petros

middle: C

last: Karakousis


title: Jurkat cell exosomes bound by either CD47 or CD63 harbor different RNA content

city: BETHESDA

first: abdel

last: Elkahloun

address: 50, SOUTH DRIVE

institute: NHGRI-NIH

summary: xtracellular vesicles (EVs) mediate cell-cell communication including the intercellular transfer of RNAs, which alter gene expression in target cells. However, heterogeneity in the size, density, and composition of EVs has limited progress towards defining their physiological functions and utility as disease-specific biomarkers. CD63 and MHC-1 are widely used as markers to purify EVs. CD47 is also present on EVs and alters their effects on target cells, suggesting that specific surface markers define functionally distinct EVs. This hypothesis was addressed by comparing the properties of Jurkat T cell EVs captured using CD47, CD63, and MHC-1 antibodies. These EV subsets have similar sizes but divergent RNA contents.

overall_design: Jurkat cell exosomes where bound by either CD47 or CD63 antibidies and conpared to their un-bound exosomes

first: Sukhbir

last: Kaur

first: Abdel


title: Gene Expression of Primary Human Type I Alveolar Epithelial Cells Exposed to Bacillus anthracis, Sterne endospores

city: Oklahoma City

first: J.

middle: Leland

last: Booth

state: OK

address: 800 N. Research Parkway

department: Internal Medicine Dept., Pulmonary and Critical Care Div.

institute: Oklahoma University Health Sciences Center

summary:
The lung is the entry site for Bacillus anthracis in inhalation anthrax, the most deadly form of the disease. Spores must escape through the alveolar epithelial cell (AEC) barrier and migrate to regional lymph nodes, germinate and enter the circulatory system to cause disease. Several mechanisms to explain alveolar escape have been postulated, and all these tacitly involve the AEC barrier. In this study, we incorporate our primary human type I AEC model, microarray gene profiling and gene enrichment analysis to study the response of AEC to B. anthracis, (Sterne) spores at 4 and 24 hours post-exposure. Spore exposure altered gene expression in AEC after 4 and 24 hours and differentially expressed genes (±1.3 fold, p ≤ 0.05) included CCL4/MIP-1β (4 hours), CXCL8/IL-8 (4 and 24 hours) and CXCL5/ENA-78 (24 hours). Gene enrichment analysis revealed that pathways involving cytokine or chemokine activity, receptor binding, and innate immune responses to infection were prominent. Microarray results were confirmed by qRT-PCR and multiplex ELISA assays. Chemotaxis assays demonstrated that spores induced the release of biologically active neutrophil and monocyte chemokines, and that CXCL8/IL-8 was the major neutrophil chemokine. The small or sub-chemotactic doses of CXCL5/ENA-78, CXCL3/GROββ and CCL20/MIP-3α may contribute to chemotaxis by priming effects.  These data provide the first whole transcriptomic description of the human type I AEC initial response to B. anthracis spore exposure, and contribute to an increased understanding of the role of AEC in the pathogenesis of inhalational anthrax.
We used microarrays to create a whole transcriptomic description of the response of primary human type I alveolar epithelial cells to B. anthracis spore exposure and demonstrated that several of the most upregulated differentially expressed genes included those for neutrophil and monocyte chemokines.

overall_design: Primary human type I alveolar epithelial cells isolated from the lungs of deceased donors were infected with 1 × 10^6 cfu/ml (MOI ≈ 2) Bacillus anthracis, Sterne strain 7702 (pX01+, pX02-) endospores in fresh growth medium containing antibiotics, and incubated for 4 and 24 h in a humidified incubator at 37°C in 5% CO2.  Mock treated (negative control) cells received a volume of spore diluent (sterile di-water) equal to that of the spore treated cells.  At the end of incubation, the cell monolayers were washed twice with PBS and lysed by addition of 700 μl/well QIAzol lysis reagent.  Samples were processed into purified total RNA, which was reverse transcribed into cDNA and further amplified.  Samples were fragmented and biotinylated for hybridization with Affymetrix GeneChip HuGene 2.0 ST Array, Format 100, chips. Array data was log2 transformed, quantile normalized and had batch effects removed for final analysis.

first: John

middle: L

first: Elizabeth

middle: S

last: Duggan

first: Jordan

last: Metcalf

first: Dennis

middle: M

last: Burian

first: Mikhail

last: Dozmorov


title: ZFN engineered hiPSC with the FTDP-17 associated MAPT IVS10+16 mutation w/wo additional P301S mutation

status: Public on Aug 01 2018

city: Beerse

first: An

last: De Bondt

address: Turnhoutseweg 30

country: Belgium

institute: Janssen Pharmaceutica

summary:
The development of an effective therapy against tauopathies like Alzheimer’s disease (AD) and frontotemporal dementia (FTD) remains challenging, partly due to limited access to fresh brain tissue, the lack of translational in vitro disease models and the fact that underlying molecular pathways remain to be deciphered. Several genes play an important role in the pathogenesis of AD and FTD, one of them being the MAPT gene encoding the microtubule-associated protein tau. Over the past few years, it has been shown that induced pluripotent stem cells (iPSC) can be used to model various human disorders and can serve as translational in vitro tools. Therefore, we generated iPSC harboring the pathogenic FTDP-17 (frontotemporal dementia and parkinsonism linked to chromosome 17) associated mutations IVS10+16 with and without P301S in MAPT using Zinc Finger Nuclease technology. Whole transcriptome analysis of MAPT IVS10+16 neurons reveals neuronal subtype differences, reduced neural progenitor proliferation potential and aberrant WNT signaling. Notably, all phenotypes were recapitulated using patient-derived neurons. Finally, an additional P301S mutation causes an increased calcium bursting frequency, reduced lysosomal acidity and tau oligomerization.
Altogether, these tau mutant iPSC lines allow us to study IVS10+16 and P301S mutations in an isogenic background and to unravel a potential link between pathogenic 4R tau expression and FTDP-17.

overall_design:
This study includes 48 samples. There are 16 treatments considered, each with at least three biological replicates.

ZFN engineered (IVS10+16, monoallelic) and FTD patient-derived (IVS10+16, monoallelic) hiPSC have been differentiated into neurons using an established cortical differentiation protocol (PMID:22976355) with only minor modifications. Patient V97 (patient 1) and TSM (patient 2) have been described in more detail in PMID:26136155 and Verheyen et al., submitted
Cells were lysed either at neural progenitor stage (NPC), which corresponds to DIV31 of hiPSC differentiation, or 5 weeks (W5) after plating of NPCs (DIV65 from hIPSC differentiation) and subjected to microarray
Sigma CTR  = control iPSC line provided by Sigma (iPSC0028)
Sigma IVS10 = gene edited Sigma line with a MAPT mutation (IVS10+16) using Zinc Finger Nucleases (ZFN)
Patient IVS10 V97 = patient 1 (PMID:26136155; Verheyen et al., submitted)
Patient IVS10 TSM = patient 2 (PMID:26136155; Verheyen et al., submitted)

Time point represents weeks after plating of neural progenitors (NPCs);
NPC = lysis 1 day after plating
Wk3 = lysis 3 wks after plating NPCs = ± DIV51 from hiPSC differentiation
Wk5 = lysis 5 wks after plating NPCs = ± DIV65 from hiPSC differentiation
Wk7 = lysis 7 wks after plating NPCs = ± DIV80 from hiPSC differentiation

last: Verheyen

first: Joke

last: Reumers

first: Kirsten

last: Van Hoorde

first: Annick

last: Diels

first: Ilse

last: Van Den Wyngaert

first: Ronald

last: De Hoogt

first: Jacobine

last: Kuijlaars

first: Louis

last: De Muynck

first: Alexis

last: Brettevill

first: Steffen

last: Jaensch

first: Alfredo

last: Cabrera-Socorro

first: Mark

last: Gerber

first: Jason

last: Gustin

first: Selena

last: Wray

first: Andreas

last: Ebneth

first: Peter

last: Roevens

first: Ines

last: Royaux

first: Pieter

middle: J

last: Peeters


title: ZFN engineered hiPSC with the FTDP-17 associated MAPT IVS10+16 mutation w/wo additional P301S mutation and comparison of FTDP-17 IVS10+16 patient derived hiPSC and ZFN engineered hiPSC

first: An

last: De Bondt


title: Identifying SC1-regulated mRNA and lncRNA in the J1 mESCs

city: Taiyuan

first: Yongyan

last: Wu

state: Shanxi

address: No.85 South Jiefang Road, Taiyuan, Shanxi, China

department: Department of Otolaryngology Head & Neck Surgery, The First Hospital

institute: Shanxi Medical University

summary: It has been demonstrated that SC1 (Pluripotin) promotes self-renewal of mouse embryonic stem cells, however, the target genes of SC1 are not fully understood.  To better understand the downstream target genes of SC1, we performed Microarray analysis to identify their downstream targets. The data show the genes regulated by SC1.

overall_design: J1 mESCs maintained in  medium containing 1000 U/mL LIF and supplemented without or with SC1 for 6 hours, then total RNA was extracted for microarray (including mRNA and lncRNA) analysis.

first: Qing

last: Wei

first: Zhiying

last: Ai

first: Xiaoyan

last: Shi

first: Zekun

last: Guo


title: Histone H3.3K27M mutation activates multiple cancer/testis antigens

city: macau

first: gang

last: li

state: macau

address: N22  Research Building, Faculty of Health Sciences (FHS),  University of Macau,  Avenida de Universidade, Taipa, Macau, China

department: faculty of health and science

institute: university of macau

summary: Lysine27Methionine mutations (K27M) in the histone H3 (H3.3 and H3.1) are highly prevalent in pediatric high-grade gliomas (HGG). This study found H3.3K27M caused the upregulation of multiple cancer/testis (CT) antigens, include IL13RA2 and VCX family proteins. Overexpression of VCX3A/B stimulates the expression of genes involved in immune response.

overall_design: Total RNA was extracted from Res259 cells stably expressing H3.3K27M, pCMV6-Entry (empty vector), different forms of GFP-VCX3A/B, or GFP (as control), and subjected to an Illumina HT12.2 Bead CHIP array analysis.

first: Houliang

last: Deng

first: Gang

last: Li


title: Gene Expression of MCF10A cells expresing ERAS

city: Madrid

first: Manuel

last: Navarro

address: Av. Complutense 40

department: Molecular Oncology

country: Spain

institute: CIEMAT

summary:
ERAS (Embryonic stem (ES) cell-expressed Ras) is a constitutively active member of the Ras family that is not expressed in adult tissues, and has been involved in breast cancer.
ERAS was introduced in breast MCF10A cells using a lentiviral vector under the control of the beta actin promoter

overall_design: Comparison of MCF10A cells, WT (control) and cells permanently expressing ERAS under the control of the beta-actin promoter.

first: Angel

last: Ramírez

first: Cristian

last: Suárez-Cabrera


title: Effect of peripherally-derived macrophages in adult microglia (mouse cells)

city: Montreal

first: Andrew

last: Greenhalgh

state: Quebec

address: Montreal General Hospital, 1650 Cedar Ave

country: Canada

institute: The Research Institute of the McGill University Health Center

summary:
Infiltrating monocyte derived macrophages (MDMs) and resident microglia dominate CNS injury sites. We show that MDMs and microglia can directly communicate to modulate each other’s function.  Also, the presence of MDMs in CNS injury suppresses microglia-mediated phagocytosis and inflammation. We suggest that macrophages infiltrating the injured CNS provide a mechanism to control acute and chronic microglia-mediated inflammation, which could otherwise drive damage in a variety of CNS conditions.
To understand the global effects of macrophage communication to microglia, we transcriptionally profiled activated adult mouse microglia in the presence or absence of macrophages with and without an inflammatory stiumulus (LPS)

overall_design: Bone marrow-derived macropages and adult microglia from C57BL/6 male mice were cultured seperately for 7 days. On the 7th day, cells were placed together in a bilmaniar culture sytem for 24h hours, with or without an inflammatory stimulus (LPS)

middle: D

first: Sam

last: David


title: Antibiotic-induced acceleration of type 1 diabetes alters maturation of innate intestinal immunity

city: New York

first: Thomas

last: Battaglia

state: NY

address: 423 E 23rd Street

institute: NYU School of Medicine

summary: The early-life intestinal microbiota plays a key role in shaping host immune system development. We found that a single early-life antibiotic course (1PAT) accelerated Type 1 diabetes (T1D) development in male NOD mice. The single course had strong and persistent effects on the intestinal microbiome, selecting for a highly metabolically active metagenome, with altered hepatic and serum metabolites. The exposure led to differential ileal and hepatic histone modification, and perturbed ileal gene expression, strongly affecting the normal maturational pattern. Earliest effects involved specific genes in innate immune pathways, with later effects on adaptive immunity. Microbiome analysis revealed four potential T1D-protective taxa and four T1D-accelerating taxa, and a network linking specific microbial taxa to differences in ileal gene expression was identified. This simplified animal model has improved understanding of the mechanisms by which early-life gut microbiome perturbations alter host intestinal responses, contributing to T1D.

overall_design: Nanostring gene expression analysis was performed on RNA extracted from the terminal ileum of control, PAT1 and PAT3 mice from P12 to P42 of life.

first: Xuesong

last: Zhang

first: Jackie


title: NK cells actively control HIV-1 DNA reservoir

first: Maria

middle: Libera

last: Ascierto

address: 5500 Orleans Street

department: Oncology

institute: Johns Hopkins

summary: The size of lentiviral DNA reservoirs reflects effectiveness of immune responses against lentiviruses. So far, abundant information has been gathered on the control of HIV-1 replication. Understanding of innate mechanisms contributing to containment of HIV-DNA reservoir, however, are only partly clarified and are relevant to guide interventions for reservoir containment or eradication. We studied the contribution of Natural Killer (NK) cell functional features in HIV patients either controlling replication either spontaneously (HIC) or after progression and antiretroviral treatment (PP). An inverse correlation between HIV-DNA copy numbers (either total or integrated) in circulating CD4+ cells and NK cell function were observed. Induced IFN-gamma production and NKp46/NKp30 activating receptor-induced expression correlated inversely with reservoir size. The correlation was present not only when considering a homogeneous cohort of HIC patients, but also when PP patients were included in the analysis. Adaptive (NKG2C + CD57 + ) NK cell features were not associated with reservoir size. However a distinct set of 370 differentially expressed transcripts was found to underlie functional differences in NK cells controlling HIV-DNA reservoir size. In proof-of-principle in vitro experiments of CD4+ cell infection with HIV-1, purified NK cells with the above functional/transcriptional features displayed a 10- and 30-fold higher ability to control HIV replication and DNA burden in vitro, respectively, compared to other NK cells. Thus, NK cells with a specific functional and transcriptional signature contribute to control of HIV reservoir in CD4+ cells. Their selection, expansion and/or adoptive transfer may support strategies to eradicate HIV-1 infection or to safely deescalate antiretroviral treatment.

overall_design: Multiple samples from different patients (4 HIC, 4 PP) of purified NK cells, either resting (HIC n=4, PP n=4) or activated (HIC n=4, PP n=4) in vitro with rhIL-2, were evaluated by microarray analysis.


title: Expression profiles from chondrocytes in culture - time course

city: Baton Rouge

first: Claudia

last: Kappen

state: LA

address: 6400 Perkins Road

department: Developmental Biology

institute: Pennington Biomedical Research Center

summary:
To characterize the process of chondrocyte differentiation and maturation, we used Affymetrix GeneChip analysis to profile the dynamic changes in mRNA expression in high density cultures of primary rib chondrocytes from newborn mice. Temporal expression profiles were obtained from RNA harvested from chondrocytes cultured for 2, 6, 9, 12 and 15 days.
Progressive maturation of cells into cartilage-producing hypertrophic chondrocytes was accompanied by changes of expression for many genes, particularly genes encoding extracellular matrix components and transcription factors.

overall_design: Primary chondrocytes were isolated for culture by steril removal of rib cages from FVB embryos at gestational day 18.5 and plated at high densities in gelatin-coated 6-well culture dishes. Media was changed every other day and chondrocytes were allowed to grow up to 15 days. A total of 5 samples were analyzed, every sample representing a particular time point during culture.

last: Kruger

first: Aimee

last: Limpach


title: Growth of Bacillus subtilis under deep starvation conditions

city: Amsterdam

first: Martijs

last: Jonker

address: Science Park 904

department: Microarray Department

country: Netherlands

institute: University of Amsterdam

summary: The general assumption is that when bacteria run out of nutrients they become dormant or form spores. Here we show, using a new technique, that under deep starvation conditions non-sporulating Bacillus subtilis cells do not become dormant but continue to grow. B. subtilis can form (endo)spores and this has been regarded as the principal mechanism through which it survives long periods of nutrient depletion. However, in this study we demonstrate that non-sporulating B. subtilis cells can survive deep starvation conditions for many months. During this period, cells adopt an almost coccoid shape and become tolerant to antibiotics and oxidative stress. Interestingly, these cells appeared to be metabolically active, and transcriptome analyses indicated that their gene-expression profile differs substantially from both stationary phase cells, and exponentially growing cells. Surprisingly, using an inhibitor for cell division, we discovered that these coccoid-like B. subtilis cells are not dormant but actually grow and divide, albeit with a doubling time of ~4 days. It emerged that secreted proteases, allowing acquisition of nutrients from lysed brethren, are essential for this growth mode. In fact, nutrient levels comparable to 10,000 times diluted LB (Lysogeny broth) appeared to be sufficient to sustain this growth. The very slow growth provides an alternative strategy for B. subtilis to survive nutrient depletion and environmental stresses. We propose to call this the oligotrophic growth state. This state might be common among bacterial species to survive deep starvation conditions.

overall_design: RNA-seq of  Bacillus subtilis grown in overnight culture, at log phase or after 14 days of deep starvation.

first: Declan

last: Gray

first: Pamela

last: Gamba

first: Henrik

last: Strahl

first: Leendert

last: Hamoen


title: Dpy30 regulates Myc binding to targets and Myc-driven tumorigenesis (ChIP-seq, RNA-seq)

city: Birmingham

first: Hao

last: Jiang

state: AL

address: 1825 University Blvd

department: Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

summary: It remains unclear how epigenetic modulators impact the tumorigenic potential of Myc. Here we show that the core subunits, including Dpy30, of the major H3K4 methyltransferase complexes are selectively upregulated in Burkitt lymphoma, and Dpy30 is important for efficient genomic binding of Myc. Dpy30 heterozygosity does not affect normal animal physiology, but significantly suppressed lymphomagenesis and reduced expression of a subset of key pro-survival genes when Myc is hyper-activated. Dpy30 heterozygosity also impedes cellular transformation without affecting normal cell growth. These results suggest that Myc hijacks this chromatin modulator to coordinate its oncogenic program for efficient tumorigenesis, meanwhile creating “epigenetic vulnerability”, which we then exploited by specifically targeting Dpy30’s activity to inhibit growth of the Burkitt lymphoma cell model.

overall_design: Samples 1-6 are ChIP-seq from control vs. Dpy30 KD P493-6 cells. Samples 7-22 are RNA-seq from splenic B220+ cells from mice of different genotypes

first: Zhenhua

last: Yang

first: Kushani

last: Shah

first: Keith

last: Giles

first: Alireza

last: Khodadadi-Jamayran


title: Dpy30 regulates Myc binding to targets and Myc-driven tumorigenesis

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

overall_design: Refer to individual Series


title: Hierarchical control of the IL-13 signals by STAT6 and SOX11 in lung fibroblasts (MRC-5 cells)

city: Saga

first: Satoshi

last: Nunomura

address: 5-1-1 Nabeshima

institute: Saga Medical School

summary: To identify candidates for trans-acting factors for IL-13–induced genes in lung fibroblasts, we searched transcriptional factors among IL-13–inducible molecules in lung fibroblasts

overall_design: Human normal lung fibroblast cells (MRC-5 cells) were cultured for 24 hours in the presece or absence of IL-13. A single experiment was performed.

first: Kenji

last: Izuhara

first: Yasutaka

last: Mitamura


title: Age-of-Onset Dependent Immune maturation in Pediatric Crohn Disease

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

summary:
Purpose:  To clarify the biological processes underlying variation in disease location and antimicrobial sero-reactivity across age-of onset in pediatric Crohn disease.
Methods:  We characterize the ileal global pattern of gene expression using single-end, 50bp RNA-sequencing using the Illumina HiSeq2000 in 304 treatment-naïve pediatric Crohn patients and non-IBD controls.  Reads were quantified using Kallisto with Gencodev23 annotations.  For all analyses, data were stratified by patient age-of-onset.
Results:  Performing differential analysis of all reasonably-expressed transcripts (TPM>5 in ≥5 samples, with significance defined as FDR-corrected p-value<0.05 and fold change≥1.5), we identify a robust gene signature with higher expresison of an immune gene set in older patients (≥10 years at diagnosis) compared to younger patients (<10 years at diagnosis), and a decrease in expression of antimicrobial Paneth cell-derived α-defensins.
Conclusion:  We provide evidence for maturation of mucosal Th1 immune response and loss of epithelial antimicrobial α-defensins with increasing age-of-onset.

overall_design: Ileal gene expression profiles were generated for 304 treatment-naïve pediatric Crohn patients and non-IBD controls.

first: Yael

last: Haberman-Ziv

first: Lee

last: Denson


title: Calcineurin B in CD4 T cells prevents autoimmune colitis by by negatively regulating  the JAK/STAT pathway

city: Singapore

first: Michael

last: Poidinger

address: #04-06, 8A Biomedical Grove

department: Bioinformatics

country: Singapore

institute: Singapore Immunology Network

summary: Nuclear factor of activated T-cells (NFAT) are a family of transcription factors, which are regulated by the calcium-sensing protein calmodulin and protein phosphatase Calcineurin. The different NFAT family members can have overlapping functions but also are now known to exhibit distinct functions in T cells and can influence host tolerance. In the current study, we investigated for the first time the role played by the calcineurin B (Cnb1) signaling in CD4 T cells.  We generated mice that lack selectively Cnb1 in CD4 T cells (Cnb1CD4 mice) and analyzed the immune phenotype during the ageing and in vitro studies. Disruption of CnB signal in CD4 T cells was associated with an increase of IFNγ- and IL-17-secreting cells. Antibiotic treatment reverted the spontaneous intestinal inflammation observed in Cnb1CD4 mice, indicating that microbiota is the main factor involved in colitis onset. Our data indicate that Cnb1 pathway in CD4 T cells is fundamental to maintain immune homeostasis in the colon

overall_design: Lamina Propria (LP)-colon CD45+CD3+CD4+CD44low cells were sorted from control group (CD4neg/Cnb1flox) and conditional (CD4cre/Cnb1flox) mice ( 3 independent experiments 3-5 mice/group). In particular in intestinal CD4+ T cells not fully differentiated the global gene expression analysis revealed that Cnb1 is an intrinsic negative regulator of a set of genes associated of Th1 polarization.

first: Mencarelli

last: Andrea

first: Mortellaro

last: Alessandra


title: A single cell atlas of the airway epithelium reveals the CFTR-rich pulmonary ionocyte

city: Vilnius

first: Rapolas

last: Zilionis

state: LT

address: Sauletekis av 7

department: Life Sciences Center

country: Lithuania

institute: Vilnius University

summary: The functions of epithelial tissues are dictated by the types, abundance, and distribution of the differentiated cells they contain. Attempts to restore tissue function after damage require knowledge of how physiological tasks are distributed among cell types, and how cell states vary between homeostasis, injury/repair, and disease. In the conducting airway, a heterogeneous basal cell population gives rise to specialized luminal cells that perform mucociliary clearance. We performed single cell profiling of human bronchial epithelial cells and mouse tracheal epithelial cells to obtain a comprehensive picture of cell types in the conducting airway and their behavior in homeostasis and regeneration. Our analysis reveals cell states that represent known and novel cell populations, delineates their heterogeneity, and identifies distinct differentiation trajectories during homeostasis and tissue repair. Finally, we identified a novel, rare cell type, which we call the "pulmonary ionocyte", that co-expresses FOXI1, multiple subunits of the V-ATPase, and CFTR, the gene mutated in cystic fibrosis (CF). Using immunofluorescence, signaling pathway modulation, and electrophysiology, we show that Notch signaling is necessary and FOXI1 expression sufficient to drive the production of the pulmonary ionocyte, and that the pulmonary ionocyte is a major source of CFTR activity in the conducting airway epithelium.

overall_design: Single-cell mRNA sequencing of: a) primary mouse upper airway epithelial cells under homeostasis and in a recovery time course following polidocanol induced injury (14,163 cells); b) human bronchial epithelial cells (HBECs) growns in an air-liquid interface (ALI) culture (2,970 cells); c) HBECs transduced with GFP (9,436 cells) or GFP:FOXI1 (10,330 cells) and grown in an ALI culture.

first: Lindsey

last: Plasschaert

first: Rayman

last: Choo-Wing

first: Virginia

last: Savova

first: Judith

last: Knehr

first: Guglielmo

last: Roma

first: Allon

last: Klein

first: Aron

middle: B

last: Jaffe


title: Dpy30 regulates Myc binding to targets and Myc-driven tumorigenesis (Illumina HumanHT-12 V4.0 expression)

first: Hao

last: Jiang

overall_design: Control and Dpy30 KD P493-6 cells were treated with tetracycline for 3 days (to turn off Myc). Tetracycline was thoroughly washed and cells were incubated in Tet-free medium for 4 hours. RNAs from cells before Tet treatment, after Tet treatment and right before washing Tet away, and 4h after washing Tet away, were subjected to Illumina microarray analyses.

first: Zhenhua

last: Yang


title: Microarray analysis of the molecular mechanism of anti-CD26Ab to inhibit mesothelioma cell progression

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: Treatment of malignant pleural mesothelioma (MPM) cells with anti-CD26Ab inhibits tumor progression and phase I clinical application of anti-CD26Ab resulted in prolonged disease stabilization in patients with advanced/refractory MPM. In order to elucidate the molecular mechanism of anti-CD26Ab to inhibit MPM progression, microarray analysis was performed on anti-CD26Ab treated MPM cells.

overall_design: H226 and JMN cells were treated with anti-CD26Ab for 16hr, total RNA was isolated, subjected to microarray analysis

first: T

last: Okamoto

first: C

last: Morimoto


title: DNA methylation analysis of colorectal cancer SW48/YB5 cell line treated with the HH1 compound

status: Public on Jul 31 2018

city: Camden

first: Jaroslav

last: Jelinek

state: NJ

address: 403 Haddon Avenue

department: Research Labs

institute: Coriell Institute for Medical Research

type: Methylation profiling by high throughput sequencing

summary: YB5 is a colon cancer cell line derived from the SW48 colon cancer cell line and contains a DNA methylated and silenced CMV promoter driving expression of a GFP reporter. The cells were treated with 10 micromolar concentration of the HH1 compound or with DMSO as a control. Reduced representation bisulfite sequencing (RRBS) was performed after the treatment to analyze DNA methylation at CpG sites.

overall_design: Biological triplicates were performed for HH1 and DMSO control. Untreated cells were analyzed in a biological duplicate.

first: Hanghang

last: Zhang

first: Somnath

last: Pandey

first: Meghan

last: Travers

first: Hongxing

last: Sun

first: Yasuyuki

first: Takahiro

last: Sato

first: Judit

last: Garriga

first: Bela

last: Patel

first: Jozef

last: Madzo

first: Noël

last: Raynal

first: Yi

first: Wayne

last: Childers

first: Magid

last: Abou-Gharbia

first: Stephen

last: Baylin

first: Cynthia

last: Zahnow

first: Xavier

last: Graña

first: Jean-Pierre

last: Issa


title: DNA methylation in mouse ovarian carcinoma ID8 cell line.

first: Jaroslav

summary: We performed DNA methylation profiling at CpG sites in ID8 mouse ovarian cancer cells.

overall_design: Three independent samples of the ID8 cell line were analyzed in parallel.

first: Hanghang

last: Okamoto


title: Transcript profiling upon overexpressing an AP2/ERF transcription factor Rap2.9  in A. thaliana

city: Erlangen

first: Haina

state: Bayern

address: Staudtstrasse 5

department: Division of biochemistry

country: Germany

summary: The genome of Arabidopsis contains 122 ERF transcription factor genes, some of which play diverse roles in the development and stress responses. A previous transcriptome analysis of Arabidopsis revealed that gene expression under combinatory stress conditions is not predictable from the combination of individual stresses (GSE46760). Searching for commonly regulated genes verified that only 11 genes were regulated in all stress combinations . Among these 11 genes, Rap2.9 (AT4G06746) was down-regulated under all stress conditions. Transgenic Arabidopsis thaliana lines overexpressing Rap2.9 under CaMV 35S promotor were generated, and the microarray analysis revealed that overexpression of Rap2.9 in A. thaliana plants causes massive reprogramming of transcription resulting in the alteration of the hormonal homeostasis and imbalances in signalling cascades related to stress response. Further analysis also revealed that Rap2.9 played an crucial role in plant development and stress tolerance in Arabidopsis plants.

overall_design: For microarray analysis, transgenic Arabidopsis plants (35S::Rap2.9-GFP) and wild-type plants (Col-0) were grown in the same time and same condition for 54 days. Leaf samples were immediately frozen in liquid nitrogen and stored at -80°C. For each genotype, 4 biological replicates have been sampled for RNA extraction.

first: Christian

last: Prasch

first: Ulrich

last: Hirschmüller

last: Reid

first: Uwe

last: Sonnewald


title: Human Feto-placental Arterial and Venous Endothelial Cells are Differentially Programmed by Gestational Diabetes Mellitus Resulting in Cell-specific Barrier Function Changes

city: Graz

first: Silvija

last: Tokic

address: Auenbruggerplatz 14

institute: Medical University of Graz

summary:
We performed genome-wide methylation analysis of primary feto-placental arterial and venous endothelial cells from healthy (AEC and VEC) and GDM complicated pregnancies (dAEC and dVEC). Parallel transcriptome analysis identified variation in gene expression linked to GDM-associated DNA methylation, implying a direct functional link. Pathway analysis found that genes altered by exposure to GDM clustered to functions associated with ’Cell Morphology’ and ’Cellular Movement’ in both AEC and VEC. Further functional analysis demonstrated that GDM exposed cells have altered actin organization and barrier function.
Our data indicate that exposure to GDM programs atypical morphology and barrier function in feto-placental endothelial cells by DNA methylation and gene expression change. The effects differ between AEC and VEC, indicating a stringent cell-specific sensitivity to adverse exposures associated with developmental programming in utero.

overall_design: Primary human feto-placental endothelial cells form arteries (AEC) and veins (VEC) were isolated after healthy pregnancy (AEC, VEC) and after a pregnancy complicated by Gestational Diabetes Mellitus (dAEC, dVEC). Total RNA was isolated and subjected to microarray analysis.

last: Cvitic

first: Lavinia

last: Gordon

first: Boris

last: Novakovic

first: Christine

last: Ulz

first: Magdalena

last: Mühlberger

first: Francisca

middle: I

last: Diaz-Perez

first: JiHoon

middle: E

last: Joo

first: Vendula

last: Svendova

first: Michael

last: Schimek

first: Slave

last: Trajanoski

first: Richard

last: Saffery

first: Ursula

last: Hiden

first: Gernot

last: Desoye


title: Expression changes with JAK2V617F and TNF receptor block in a murine model of MPN

city: Salt Lake City

middle: W.

last: Deininger

state: UT

address: 2000 Circle of Hope HCI 4280

department: Hematology & Hematologic Malignancies

institute: Huntsman Cancer Institute

summary:
We analyzed expression changes between JAK2V617F positive bone marrow cells and JAK2V617F negative cells
We further analyzed how TNF receptor (receptor 1 or receptor 2) block influenced these changes in JAKV617F positive relative to JAK2V617F negative

overall_design: Bone marrow was harvested from Balb/c mice with established JAK2V617F (GFP tagged) MPN. Cells were treated for 16 hours with our without TNFR1 or TNFR1 blocking antibodies (BAs). Cells were then sorted for Lin-Kit+ cells and subdivided into GFP+ and GFP- fractions and subject to RNA isolation and microarray analysis

first: William

last: Heaton

first: Russell

last: Bell


title: Transcriptome analysis of the sigD deletion mutant using the Agilent platform arrray  [Agilent-025748]

city: Kyoto

first: Masayuki

last: Inui

address: 9-2 Kizugawadai, Kizugawa

institute: Research institute of Innovative Technology for the Earth (RITE)

summary: (Coryno)mycolate is a α-branched, β-hydroxylated long-chain fatty acid specifically synthesized in bacteria in the suborder Corynebacterineae of the phylum Actinobacteria. It forms an outer membrane and functions as a permeability barrier conferring pathogenic mycobacteria to resistance to antibiotics. Whereas mycolate biosynthetic pathway has been intensively studied, the studies on the transcriptional regulation of genes involved in the pathway are limited. Here, we report that the previously uncharacterized extracytoplasmic function σ factor, σD, is a key regulator of the mycolate synthetic genes in Corynebacterium glutamicum in the suborder. Chromatin immunoprecipitation with microarray analysis detected σD-binding regions in the genome, establishing a consensus promoter sequence for σD recognition. The σD regulon comprises acyl-CoA carboxylase subunits, acyl-AMP ligase, polyketide synthase, and mycolyltransferases, all of which are involved in mycolate synthesis. Actually, deletion or overexpression of sigD encoding σD modified the amount of extractable mycolate. Immediately downstream of sigD, rsdA  encoded anti-σD and was under the control of a σD-dependent promoter. Another σD regulon member, L,D-transpeptidase, conferred lysozyme resistance. Thus, σD modifies cell wall composition and enhances mycolate synthesis to provide resistance to environmental stress.

overall_design: Gene expression profile of the wild type at the exponential phase was compared with that of the sigD deletion mutant. Two independent experiments were performed.

first: Koichi

last: Toyoda


title: Transcriptome analysis of the sigD deletion mutant using the oligo array

overall_design: Gene expression profile of the wild type at the exponential phase was compared with that of the sigD deletion mutant. Three independent experiments were performed.


title: Analysis of the contributions of PKL, CLF, and PIE1 to gene expression, H2A.Z levels, and H3K27me3 levels in Arabidopsis

city: Bethesda

first: Benjamin

last: Carter

address: 10 Center Drive

department: NHLBI

institute: National Institutes of Health

summary: ChIP-seq was performed using anti-H3, anti-H3K27me3, and anti-H2A.Z antibodies in three-week-old WT, pkl-1, clf-28, and pie1-5 shoots using paired-end sequencing. Strand-specific RNA-seq was performed on RNA extracted from the same biological samples.

overall_design: RNA-seq analyses used three independent biological replicates. ChIP-seq analyses used two independent biological replicates. Four genetic backgrounds were examined: WT, pkl-1, clf-28, and pie1-5.

first: Joseph

last: Ogas

first: Brett

last: Bishop

first: Roger

last: Deal

first: Heng

last: Zhang

first: Pete

last: Pascuzzi


title: Transcriptome analysis of the rsdA deletion mutant using the oligo array

overall_design: Gene expression profile of the wild type at the exponential phase was compared with that of the rsdA deletion mutant. Three independent experiments were performed.


title: Chip-chip analysis of C. glutamicum SigD

type: Genome binding/occupancy profiling by array

overall_design: ChIP-chip analyses using a strain expressing the FLAG-tagged SigD in the background of the wild type at the exporenatial phases. Two independent experiments were performed.


title: Overexpression of sigD in the wild type

overall_design: Comparison of gene expression profiles of the wild type before and after sigD overexpression at the exponential phase. Four independent experiments were performed.


title: Identification of selective inhibitors for diffuse-type gastric cancer cells by screening of annotated compounds in E-cadherin/p53 double conditional knockout mice

city: Bunkyo-ku

first: Kaoru

last: Mogushi

state: Tokyo

address: 1-5-45 Yushima

department: Department of Molecular Oncology

institute: Tokyo Medical and Dental University

summary: Diffuse-type gastric cancer (DGC) exhibits rapid disease progression and a poor patient prognosis. We have previously established an E-cadherin/p53 double conditional knockout (DCKO) mouse line as the first genetically engineered one, which morphologically and molecularly recapitulates human DGC. In this study, we explored low-molecular-weight drugs selectively eliminating mouse DGC cells, and then validated their inhibitory effects on human DGC. We first derived mouse gastric cancer (GC) cell lines from DGC of the DCKO mice, which notably demonstrated enhanced tumorigenic activity in immunodeficient mice and acquired tolerance to cytotoxic anti-cancer agents. We next performed a synthetic lethal screening of 1535 annotated chemical compounds by using them. Comparing cell viability of the E-cadherin/p53-deficient GC and p53-deficient gastric epithelial (GE) cells under treatment with the compound library, we identified 27 candidates with specific toxicity to the GC cell lines. The most potent drug mestranol, an estrogen derivative, and other estrogen receptor modulators induced apoptotic events preceded by DNA damage only in the GC cell lines, but not in the GE. Moreover, mestranol could significantly suppress tumor growth of the GC cells subcutaneously transplanted into nude mice, consistent with longer survival time in the female DCKO mice than in the male. As expected, human E-cadherin-mutant and -low gastric cancer cells showed higher susceptibility to estrogen drugs in contrast to E-cadherin-intact ones in vitro and in vivo. These findings may lead to the development of novel therapeutic strategies targeting E-cadherin-deficient DGC.

overall_design: The E-cadherin/p53 double conditional knockout (DCKO) mice, Atp4b-Cre+;Cdh1-loxP/loxP;Trp53-loxP/loxP genotype, were established as previously reported (Shimada et al. Gut 2012). Mice bearing tumors were sacrificed, and the primary tumors were isolated. Small pieces were immediately minced from them under sterile conditions, decolonized at 4 °C overnight in DMEM/F12 media containing 10% fetal bovine sera (FBS), 100 U/ml penicillin, and 100 μg/ml streptomycin, and subcutaneously injected into the male KSN nude mice. According to the same protocols, the transplanted tumor was dissected into aliquots which were explanted on the collagen-coated plates, and cultured in the DMEM/F12 media. The MDGC4SC1, 6 and 7 cell lines were subcloned from the MDGC4 by limiting dilution in DMEM + 10% FBS. Similarly, the MDGC7, 8 and 9 cell lines were generated from the primary cancer (MDGC7 and 8) and lymph node dissemination (MDGC9) in F12 supplemented with 5% horse or bovine sera. The GIF7, 9 and 13 cell lines have previously reported (Fukamachi et al. Biochem Biophys Res Commun 2004), and maintained in DMEM + 10% FBS.

first: Shu

last: Shimada

first: Yoshimitsu

last: Akiyama

first: Mari

last: Ishigami-Yuasa

first: Hiroyuki

last: Kagechika

first: Hiromi

last: Nagasaki

first: Hiroshi

last: Fukamachi

first: Yasuhito

last: Yuasa

first: Shinji

last: Tanaka


title: Transcriptome analysis of the rsdA deletion mutant using the Agilent platform arrray  [Agilent-025748]

first: Masayuki

last: Inui

overall_design: Gene expression profile of the wild type at the exponential phase was compared with that of the rsdA deletion mutant. Two independent experiments were performed.


title: Daphnia magna CRISPR/Cas9 TRH gene knock downs transciptomic profilling

city: Barcelona

first: Bruno

last: Campos

address: jordi girona, 18, 18

department: Environmental Chemistry

institute: IDAEA-CSIC

summary: Transcriptomic profilling of 4 daphnia magna clones. One laboratory clone (Clone F +/+), one heterozygotic Clone (Clone 13 +/-) , two homozygotic Clones (Clone 16 and 17 -/-)

overall_design: 4 samples of 5 days old daphnias

first: Claudia

last: Rivetti

first: Carlos

last: Barata


title: Genome-wide analyses of C. glutamicum SigD

platform_organism:
Corynebacterium glutamicum
Corynebacterium glutamicum R

overall_design: Refer to individual Series


title: F508del homozygous cystic fibrosis patients and healthy controls

city: Montpellier

first: Albertina

last: DE SARIO

address: 641, av du doyen Gaston Giraud

department: PhyMedExp

institute: INSERM 1046-CNRS 9214-Univ Montpellier

type: Methylation profiling by genome tiling array

summary:
Using the 450K BeadChIP, we profiled DNA methylation in nasal epithelial cells collected from CF patients homozygous for the CFTR p.Phe508del mutation and healthy controls. We replicated DNA methylation at CpG sites by pyrosequencing. Patients were stratified according to their lung function (forced expiratory volume in 1 second). Our study (i) points to the importance of genes responsible for the integrity of the epithelium and the inflammatory and immune responses to explain lung disease variability in CF, (ii) highlights new candidate genes potentially involved in lung disease severity, while it corroborates the role of known modifier genes, and (iii) suggests that CF-associated dynamic changes of DNA methylation are prominent in transcriptionally active genomic regions.
Bisulphite converted DNA from the 48 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

overall_design: 32 cystic fibrosis patients (16 mild , 8 intermediary, 8 severe lung disease) and 16 healthy controls

first: Milena

last: Magalhaes

first: Jörg

last: Tost

first: Fanny

last: Pineau

first: Isabelle

last: Rivals

first: Florence

last: Busato

first: Nathan

last: Alary

first: Laurent

last: Mely

first: Sylvie

last: Leroy

first: Marlène

last: Murris

first: Davide

last: Caimmi

first: Mireille

last: Claustres

first: Raphaël

last: Chiron

last: De Sario


title: Gene expression profiling of LPS and menthol treatment on mouse macrophages

city: Boston

first: Hoon

last: Ryu

address: 150 S. Huntington Ave.

institute: Boston University School of Medicine

summary: To characterize the effect of menthol on macrophages, comprehensive microarray analysis was performed in RAW 264.7 macrophage.

overall_design: RAW 264.7 macrophage cells were treated with menthol or control for 1 hr and followed by induction with LPS (100ng/ml) for 6 hrs.

first: Jayoung

last: Kim


title: Identification of target mRNAs of amyotrophic lateral sclerosis associated miR-1825 in HEK293 cells

status: Public on Jul 30 2018

city: Ulm

first: Axel

last: Freischmidt

address: Albert-Einstein-Allee 11

department: Neurology

institute: Ulm University

summary: In previous studies, miR-1825 has been found to be downregulated in the serum of familial and sporadic patients with amyotrophic lateral sclerosis (ALS). In this study, we aim to identify the target mRNAs of miR-1825 using a combination of proteomic and transcriptomic approaches.

overall_design: The transcriptome of HEK293 cells transfected with a miR-1825-mimic (n = 6) was compared to HEK293 cells transfected with a control RNA (n = 6) using the Affymetrix GeneChip™ Human Gene 2.0 ST Arrays.

first: Anika

last: Helferich

first: Karlheinz

last: Holzmann

first: Jochen

middle: H

last: Weishaupt


title: RNA-seq of muscle Fibro-Adipogenic Progenitor subpopulations and bulk from different injury contexts

city: San Diego

first: Sole

last: Gatto

state: CA

address: 12636 High Bluff Drive, Suite 400

institute: Monoceros Biosystems

summary:
Fibro-Adipogenic Progenitors (FAPs) are currently defined by their anatomical position, expression of non-specific membrane-associated proteins, ability to adopt multiple lineages and to perform different biological activities in response to physiological or pathological stimuli. Gene expression analysis at single cell level revealed the intrinsic heterogeneity of FAPs and uncovered discrete subpopulations (subFAPs), which can be prospectively isolated by FACS, based on the expression levels of Tie2 and Vcam1. Tie2-expressing (Tie2+) and Tie2/Vcam1 double negative (DN) subFAPs were present in unperturbed muscles and promptly expanded upon acute injury. By contrast, Vcam1-expressing subFAPs (Vcam1+) were undetectable in unperturbed muscles, but appeared “de novo” upon acute injury and expanded with a shifted kinetic compared to Tie2+ and DN FAPs. While Vcam1+ subFAPs were completely cleared upon resolution of muscle regeneration following acute injury, they persisted in chronically injured muscles from the mdx mouse model of Duchenne Muscular Dystrophy (DMD). “Nested” RNA-seq analysis of subFAPs revealed subpopulation-specific gene expression profiles that were dynamically regulated along the regeneration process, predicted specific biological activities and functional interactions with other cell types, and exhibited DMD-specific signatures. In particular, Vcam1+ subFAPs showed enrichment in fibrotic gene expression and myofibroblast markers, and their altered clearance in acutely injured muscles upon macrophage depletion was associated with fibrosis. These data reveal the individual contribution of distinct subFAPs to the physiological and pathological repair of skeletal muscles, thereby providing new insights into the pathogenesis of muscular dystrophies and targets for selective therapeutic interventions.
RNA-seq study of bulk FAPs or subFAPs isolated by Fluorescence Activated Cell Sorting (FACS) from hind limb muscles of young (3 months old) mice.
RNA-seq was performed in cells from wild type mice, either unperturbed (WT) or at 3 days post notexin-mediated intramuscular acute injury (WT-inj 3d). We also included dystrophic mice (MDX), the murine model of Duchenne Muscular Dystrophy (DMD) that provides an experimental setting for chronic muscle injury

overall_design: RNA-seq of muscle Fibro-Adipogenic Progenitor either bulk or subpopulations (Tie2+, Vcam1+, DN) from wild-type, acute and chronic injury.

first: Barbora

last: Malecova


title: Functional Genomics Analysis of Islets from Recent and Longstanding T1D Reveals the Need for Distinct Approaches to Therapy

city: Indianapolis

first: Teresa

middle: L.

last: Mastracci

institute: Indiana Biosciences Research Institute

summary: Our current understanding of the pathogenesis of T1D arose in large part from studies using the non-obese diabetic (NOD) mouse model of type 1 diabetes (T1D). Of concern, therapeutic interventions shown to significantly dampen or even reverse disease in mouse models have not successfully translated into interventions in human T1D. The present study addresses this disconnect in research translation by directly analyzing human donor islets from individuals with T1D, aiming to provide insight into disease mechanisms and identify potential target pathways for therapeutic intervention. We obtained human islets from a young individual with short-duration T1D, an older individual with long-duration T1D and three non-diabetic donors, and performed unbiased functional genomic analysis by high depth RNA sequencing on these unique cases. This analysis identified several inflammatory pathways upregulated in short-duration disease, which surprisingly included many components of innate immunity. Subsequent manipulation of one of these pathways/factors in NOD mice resulted in a significant reduction in diabetes progression when inhibition occurred early in disease progression. Taken together our data demonstrates that the direct analysis of human islets is essential for identifying relevant and promising novel targets for translation into effective therapeutic interventions for human T1D.

overall_design: 5 human islets of Langerrhans preparations. 3 in normo-glycemic individual, one individual with a long duration type 1 diabetes and one individual with short duration type 1 diabetes

first: Jean-Valery

last: Turatsinze

first: Decio

last: Eizirik

first: Raghavendra

middle: G

last: Mirmira


title: Gene expression data of human gastric tumors

first: Vivien

last: Koh

address: 1E Kent Ridge Road

institute: National University Health System

summary:
Tumors of advanced gastric cancer patients were biopsied and subjected to gene expression profiling using the Affymetrix Human Genome U133 Plus 2.0 Arrays. Patients were then segregated into G1, G2 or G3 groups based on their tumor genomic profiles. Patients in the G1 and G3 cohorts were assigned SOX (oxaliplatin plus S-1) chemotherapy whereas those in the G2 cohort were given SP (cisplatin plus S-1) regimen.
This bench-to-bedside effort indicated the feasibility of using molecular profiling to tailor treatment for advanced gastric cancer.

overall_design: Total RNA was isolated from biopsied tumors and profiled on the Affymetrix Human Genome U133 Plus 2.0 microarray platform following manufacturer's instructions.

first: Wei-Peng

last: Yong


title: Transcriptional characterization of maize roots in response to nitrate (NO3-), Water-Extractable Humic Substances (WEHS) and NO3-+WEHS.

city: Verona

first: Anita

last: Zamboni

address: Strada Le Grazie, 15

department: Biotechnology

country: Italy

institute: University of Verona

summary:
Soil humic substances are known to positively influence plant growth and nutrition. In particular, low-molecular fractions have been shown to increase NO3- uptake and PM H+-ATPase activity and alter expression of related genes. Changes in maize root transcriptome due to treatment with nitrate (NO3-), Water-Extractable Humic Substances
(WEHS) and NO3-+WEHS were analyzed.

overall_design:
5 dd-old maize plants were treated for 4 and 8 hours with nutrient solution containing 0.5 mM Ca(NO3)2 (NO3- treatment), 5 mg Corg L-1 WEHS (WEHS treatment) and  0.5 mM Ca(NO3)2 and  5 mg Corg L-1 WEHS (NO3-+WEHS treatment).
Three different biological replicates were used for each sample repeating the treatment experiment three times. All samples were obtained pooling roots of six plants.

first: Laura

last: Zanin

first: Nicola

last: Tomasi

first: Davide

last: Sega

first: Zeno

last: Varanini

first: Roberto

last: Pinton


title: Root transcriptional profile of wheat seedlings in response to Fe, S and dual (Fe and S) deficiencies.

summary: The comparison of transcriptional profiles of roots grown under Fe, S and dual deficiency with those obtained for roots of control plants (grown in a complete nutrient solution) allowed identifying the transcripts differentially expressed in response to each deficiency.

overall_design: Transcriptional profiles were obtained using roots of 5-day-old wheat seedlings grown for 14 additional days in four different nutritional conditions (control, C, 1.2 mM sulfate and 80 µM FeIII-EDTA; Fe deficiency, Fe, 1.2 mM sulfate and 0 µM FeIII-EDTA; S deficiency, S, 0 mM sulfate and 80 µM FeIII-EDTA; dual deficiency, D, 0 mM sulfate and 0 µM FeIII-EDTA).

first: Silvia

last: Celetti

first: Sara

last: Zenoni

first: Stefania

last: Astolfi


title: Acquisition of Pluripotency by HAG1-mediated Epigenetic Reprogramming of Key Potency Factor-encoding Loci in Arabidopsis

status: Public on Jul 29 2018

city: Düsseldorf

first: Jiyun

last: Kim

address: Universitätsstr. 1

department: Biology

institute: HHU

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


title: Global gene-expression profiles of wild type (WT; Columbia-0; Col) and hag1 in the course of de novo shoot regeneration

summary: Global gene-expression profiles of WT and hag1 were generated by RNA seq to understand the role of HAG1 in de novo shoot regeneration.

overall_design: WT and hag1 roots (R), 4 d CIM-incubated root explants (C), 4 d CIM-incubated + 2 d SIM (S)- and 2 w SIM (S2W)-incubated root explants were collected. Total RNA was isolated (OD260/280 ratio of 1.8 to 2.2) and RNA libraries were prepared by Beijing Genomics Institute (BGI) using standard Illumina protocols.

first: Yoo-Sun

last: Noh

first: Bosl

first: Ji-Yun

first: Woorim

last: Yang


title: A revised airway epithelial hierarchy includes CFTR-expressing ionocytes

first: Adam

last: Haber

state: Massachusetts

address: 665 Huntington Ave, HSPH Building 1, Room 305

institute: Harvard T. H. Chan School of Public Health

summary: Airways conduct gases to the lung and are disease sites of asthma and cystic fibrosis. Here we study the cellular composition and hierarchy of the mouse tracheal epithelium by single-cell RNA-sequencing (scRNA-seq) and in vivo lineage tracing. We identify a rare cell type, the Foxi1+ pulmonary ionocyte; functional variations in club cells by proximodistal location; a distinct cell type in high turnover squamous epithelial structures that we term 'hillocks'; and disease-relevant subsets of tuft and goblet cells. We developed 'pulse-seq' , combining scRNA-seq and lineage tracing, to show that tuft, neuroendocrine and ionocyte cells are continually and directly replenished by basal progenitor cells. Ionocytes are the major source of transcripts of the cystic fibrosis transmembrane conductance regulator in both mouse (Cftr) and human (CFTR). Knockout of Foxi1 in mouse ionocytes causes loss of Cftr expression and disrupts airway fluid and mucus physiology, phenotypes that characterize cystic fibrosis. By associating cell-type-specific expression programs with key disease genes, we establish a new cellular narrative for airways disease.

overall_design: To understand normal tissue homeostasis, untreated cells were profiled using both 3'-droplet-based and full length plate-based single-cell RNAseq, in combination with genetic reporter-based lineage tracing.

first: Daniel

middle: T

last: Montoro

first: Moshe

last: Biton

first: Vladimir

last: Vinarsky

first: Sijia

last: Chen

first: Jorge

last: Villoria

first: Noga

last: Rogel

first: Purushothama

last: Rao Tata

first: Steven

last: Rowe

first: John

middle: F

last: Engelhardt

first: Aviv

last: Regev

first: Jayaraj

last: Rajagopal

first: Brian

last: Lin

first: Susan

last: Birket

first: Feng

last: Yuan

first: Hui Min

last: Leung

first: Grace

last: Burgin

first: Alexander

last: Tsankov

first: Avinash

last: Waghray

first: Michal

last: Slyper

first: Julia

last: Waldman

first: Lan

last: Nguyen

first: Danielle

last: Dionne

first: Orit

last: Rozenblatt-Rosen

first: Hongmei

last: Mou

first: Manjunatha

last: Shivaraju

first: Herman

last: Bihler

first: Martin

last: Mense

first: Guillermo

last: Tearney


title: Genome-wide maps of histone H3 acetylation (H3Ac) in wild type (WT; Columbia-0; Col) and hag1 calli

first: Jiyun

last: Kim

summary: Genome-wide histone H3Ac maps of WT and hag1 calli were generated by chromatin immunoprecipitation (ChIP) followed by high-throughput DNA sequencing (ChIP seq) to understand the role of HAG1 in the reprogramming of the epigenome during callus formation.

overall_design: Examination of H3Ac levels in WT and hag1 calli.

first: Yoo-Sun

last: Noh

first: Bosl

first: Ji-Yun

first: Woorim

last: Yang


title: rne Rhodobacter sphaeroides

status: Public on Jul 27 2018

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

summary: Comparison of wild type and mutant strain with temperature-sensitive RNase E. Goal: to study the effect of RNase E on the transcriptome

overall_design: Total of 12 samples. Wild type and mutant were grown to exponential phase at 32 °C or 42° degree celsius. Biological triplicates were performed

middle: U

first: Carina

last: Reuscher

first: Kerstin

last: Haberzettl

first: Lennart

last: Weber

first: Gabriele

last: Klug


title: RNA-binding activity of TRIM25 is mediated by its PRY/SPRY domain and is required for ubiquitination

city: Edinburgh

first: Shaun

middle: Michael

last: Webb

address: 2.21 Swann Building, Kings Buildings

department: Wellcome Trust Centre for Cell Biology

institute: University of Edinburgh

summary: TRIM25 E3 ubiquitin ligase is a new RNA-binding protein. We present the first high-throughput analysis of the molecular interactomes of TRIM25. We show that TRIM25 is a bona fide RNA-binding protein that interacts with numerous coding and non-coding transcripts. This suggests that TRIM25 could play a role in the regulation of RNA metabolism.

overall_design:
We performed UV crosslinking and immunoprecipitations in HeLa cells transiently expressing T7-tagged TRIM25, followed by high-throughput sequencing of TRIM25-associated RNAs (CLIP-seq). This was done in three biological replicates.

Please note that each processed data is genrated from Trim25 and Mock dataset pairs (e.g. e.g.Trim25_exp1_significant_clusters.gtf.gz generated from both Trim25 CLIP-seq exp1 and Mock CLIP-seq exp1 ) and linked to the corresponding  Trim25 CLIP-seq sample records.

first: Nila

middle: R

last: Choudhury

first: Gregory

last: Heikel

first: Maryia

last: Trubitsyna

first: Peter

last: Kubik

first: Jakub

last: Nowak

first: Sander

last: Granneman

first: Christos

last: Spanos

first: Juri

last: Rappsilber

first: Alfredo

last: Castello

first: Gracjan

last: Michlewski


title: Differential gene expression between long-term affected and naïve flat oyster (Ostrea edulis) stocks in response to Bonamia ostreae

city: LUGO

first: Belen

last: Pardo

state: LUGO

address: Avda. Carballo Calero s/n

department: Zoology, Genetics and Physical Anthropology

institute: University of Santiago de Compostela

summary: The European flat oyster (Ostrea edulis) production has suffered a severe decline in the last decades mostly due to bonamiosis disease. The responsible parasite, Bonamia ostreae, enters the oyster immune-effector cells, the haemocytes, causing their breakage and an acute inflammatory response frequently leading to oyster death. Here, we used an oyster immune-enriched oligo-microarray to understand the haemocyte response to B. ostreae using two different oyster stocks, naïve (NS) and long-term affected (AS), evaluated at three time points, 1 day post-challenge (dpc), 30 dpc and 90 dpc, using five biological replicates per condition. A total of 213 (134 up-, 79 down-regulated) and 538 (330 up-, 208 down-regulated) regulated genes (RGs) were detected in NS and AS stocks, respectively. AS oysters showed a remarkably higher response at 1 dpc when compared to NS (507 vs 86 RGs), while more RGs were found in NS at 90 dpc (127 vs 31 RGs in AS). No RGs were detected at 30 dpc, which suggests some kind of parasite latency during infection. Further, a total of 837 genes resulted differentially expressed (DE) when comparing NS and AS profiles. The stronger response of the AS stock at the early stage might be indicative of the process of selection for resistance. Genes related to extracellular matrix and proteases inhibitors, up-regulated in the AS oysters, and those related to histones, broadly down-regulated in NS, might have an important role during the infection process. A set of 24 candidate genes potentially related to B. ostreae resistance/susceptibility were identified and they should be further validated for selection programmes aimed to control this parasitosis.

overall_design: Oysters from two strain ( Limfjord and Ortigueira) were experimentally challenged with B. ostreae, along with the corresponding non-challenged controls. The Limfjord oyster population was still naïve regarding bonamiosis in 2010 (NS: naïve stock onwards). Conversely, bonamiosis affects oysters in Ortigueira since early 1980's (AS: long-term affected stock onwards) and oysters from this bed are more resistant to B. ostreae than oysters from other geographic originsAfter challenge, haemolymph samples were taken at 3 different times after the challenge (1, 30 and 90 days). A number of 5 biological replicated for each condition (control and challenged), strain (naïve and tolerant) and sample times (1, 30 and 90 days) was taken. Samples were centrifuged (800g, 10 min, 4C) and the cell fractions (pellets) were resuspended in RNA later and stored at -20ºC after one night at 4ºC until further processing. RNA was individually extracted using RNeasy Mini Kit (Qiagen, Germany) following manufacturer's instructions with slight modifications, including two additional RPE washes and DNase digestion. For each experimental condition, the control group was pooled by combining equimolar RNA quantities of the five biological replicates, while the RNA of each challenged oyster was processed individually (five replicates). Next, 50 ng of total RNA were labeled using the Low Input Quick Amp Labeling Kit, One-Color (Cy3; Agilent Technologies). A total of 36 microarrays were used for hybridizations of 6 control (RNA pools from 2 stocks x 3 sample times) and 30 challenged oysters (5 biological replicates x 2 stocks x 3 sample times). Copy RNA (cRNA) was hybridized overnight during 17 h at 65ºC and washed with the corresponding buffers on the following day. Hybridized slides were scanned using an Agilent G2565B microarray scanner (Agilent Technologies).

first: Paolo

last: Ronza

first: Asunción

last: Cao

first: Diego

last: Robledo

first: Antonio

last: Gómez-Tato

first: José

middle: A

last: Álvarez-Dios

first: Abul

last: Hasanuzzaman

first: María

last: Quiroga

last: Villalba

first: Belén

first: Paulino

last: Martínez


title: Expression data comparing Normal Human Bronchial Epithelial Cells (NHBE) cells in states of senescence, proliferation and quiescence

city: Durham

first: Xiao-Fan

last: Wang

state: NC

address: 308 Research Drive

department: Pharmacology and Cancer Biology

institute: Duke University

summary: EGFR inhibitor Erlotinib treatment can induce NHBE into profound cell cycle arrest that include senescence and quiescence. Because senescent cells feature high senescence assocaited-beta-galactosidase(SA-β-gal) activty, which has been used as marker for FACS based collection of senescent and quiescent cells, respectively.

overall_design: After FACS sorting based on SA-β-gal activty, control (DMSO treated), quiescent (Erlotinib treated), senescent NHBE cells (Erlotinib treated) have been selected for RNA extraction and hybridization on Affymetrix microarray. We aimed to explore genes, the expression of which are specifically changed in senescence group (Erlotinib-SE), while remain similar expression pattern in both control (DMSO-CON) and quiescence (Erlotinib-Q) group.

first: Lifeng

last: Yuan


title: Effect of curaxin CBL0137 on expression of genes in MM1.S and HeLa S3 cells

status: Public on Jul 25 2018

city: Buffalo

first: Katerina

last: Gurova

address: Elm and Carlton Str

department: Cell Stress Biology

institute: Roswell Park Cancer Institute

summary: CBL0137 id non-genotoxic DNA binding compounds which directly destabilizes nucleosomes in cells.  Effect of different doses of CBL0137 on the abundance of mRNA was studied  in two cell types, multiple myeloma MM1.S and cervical carcinoma HeLa cell.

overall_design: Cells were treated with different concentrations of CBL0137 (0, 0.3, 1 and 3 microM for MM1.S; 0 and 3microM for HeLa S3) for 6 hours. All conditions were done in duplicates. RNA was isolated using TRIZOL reagent.

middle: V

first: Jianmin


title: Rtt105 promotes DNA replication by functioning as an RPA chaperone

city: Beijing

first: Qing

last: Li

address: No.5 Yiheyuan Road Haidian District

department: School of Life Science

institute: Peking University

summary: Single-stranded DNA (ssDNA) binding protein Replication Protein A (RPA) is essential for protecting ssDNA at replication forks. However, how RPA is loaded to replication forks remains unexplored. Here, we show that Regulator of Ty1 transposition protein 105 (Rtt105) binds RPA and is required for the association of RPA with replication forks. Cells lacking Rtt105 exhibit dramatic genome instability and severe defects in DNA replication. Intriguingly, both the RPA nuclear import and its ability to bind DNA replication forks were greatly compromised in rtt105 mutant cells, however, targeting RPA to the nucleus cannot rescue the defect of RPA binding to replication forks. Importantly, Rtt105 promotes the binding of RPA to ssDNA but does not associate with  the final RPA-ssDNA complex in vitro. Moreover, single-molecule studies revealed that Rtt105 affects the binding mode of RPA to ssDNA. These results support a model in which Rtt105 functions as an RPA chaperone that escorts RPA to nucleus and assemble RPA onto ssDNA at replication forks.

overall_design: To examine the distribution of CMG complex in WT and rtt105 deletion mutant cells, we used Mcm6 and Cdc45 ChIP-Seq for cells at G1 phase and S phase.

first: Shuqi

first: Zhiyun

last: Xu

first: Xuezheng

first: Jiawei

first: Chuanhe

last: Yu

first: Pu

last: Zheng

first: Haiyun

last: Gan

first: Andrei

last: Chabes

first: Di

first: Kuiming

last: Chan

first: Jianxun

last: Feng


title: ETS1 induction by the omental microenvironment promotes ovarian cancer metastasis [ChIP-Seq]

status: Public on Jul 24 2018

city: Bloomington

first: Peter

last: Hollenhorst

state: IN

address: 1001 E Third St, Jordan Hall 104

institute: Indiana University

summary: ETS1 expression is induced by the microenvironment of ovarian metastasis and this expression allows ETS1 to activate a gene expression program involved in cell invasion and epithelial mesenchymal transision.

overall_design: ChIP-sequencing to map binding sites of ETS1 in ovarian cancer cell lines HEYA8 and OVCAR8

first: Joshua

middle: P

last: Plotnik

middle: C

first: Anirban

middle: K

last: Mitra


title: Targeting the MTF2-MDM2 Axis Sensitizes Refractory Acute Myeloid Leukemia to Chemotherapy

city: Ottawa

first: William

last: Stanford

state: Ontario

address: 501 Smyth Road

institute: Ottawa Hospital Research Institute

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

Deep sequencing has revealed that epigenetic modifiers are the most mutated genes in acute myeloid leukemia (AML). Thus, elucidating epigenetic dysregulation in AML is crucial to understand disease mechanisms. Here, we demonstrate that Metal Response Element Binding Transcription Factor 2/Polycomblike 2 (MTF2/PCL2) plays a fundamental role in the Polycomb repressive complex 2 (PRC2) and that its loss elicits an altered epigenetic state underlying refractory AML. Unbiased systems analyses identified the loss of MTF2-PRC2 repression of MDM2 as central to, and therefore a biomarker for, refractory AML. Thus, immature MTF2- deficient CD34+CD38- cells overexpress MDM2, thereby inhibiting p53 that leads to chemoresistance due to defects in cell cycle regulation and apoptosis. Targeting this dysregulated signaling pathway by MTF2 overexpression or MDM2 inhibitors sensitized refractory patient leukemic cells to induction chemotherapeutics and prevented relapse in AML patient-derived xenograft (PDX) mice. Therefore, we have uncovered a direct epigenetic mechanism by which MTF2 functions as a tumor suppressor required for AML chemotherapeutic sensitivity and identified a potential therapeutic strategy to treat refractory AML.

overall_design: Refer to individual Series


title: Large-scale single cell mapping of the thymic stroma identifies a new thymic epithelial cell lineage [ATAC-seq]

status: Public on Jul 23 2018

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary: T cell development and selection is orchestrated in the thymus by a specialized niche of diverse stromal populations. By transcriptional single cell sorting, we de novo characterize the entire stromal compartment of the thymus. We identified dozens of cell states within the thymic stroma, with thymic epithelial cells (TEC) showing the highest degree of heterogeneity. Our analysis highlights four major medullary TEC (mTEC I-IV) populations, with distinct molecular functions, epigenetic landscapes and lineage regulators. Specifically, mTEC-IV constitutes a new and highly divergent TEC lineage with molecular characteristics of the gut chemosensory epithelial tuft cells. Mice deficient of Pou2f3, a tuft cells master regulator, resulted in complete and specific depletion of mTEC-IV, without affecting other TEC populations. Overall, our study comprehensively defines all stroma cells in the thymus and identifies a new TEC lineage associated with chemosensory properties that may potentially link the adaptive immune system to environmental and neurological signals.

overall_design: Transcriptional profiling of single cells from the stroma of mouse thymus, generated from deep sequencing of tens of thousands of cells, reveled 4 subpopulations of medullary epithelial cells. ATAC-seq assay profile the accessible chromatin landscape of these subpopulation.

first: Jakub

last: Abramson

first: Chamutal

last: Bornstein

first: Shir

last: Nevo

first: Amir

last: Giladi

first: Noam

last: Kadouri


title: ETS1 induction by the omental microenvironment promotes ovarian cancer metastasis


title: Targeting the MTF2-MDM2 Axis Sensitizes Refractory Acute Myeloid Leukemia to Chemotherapy [ChIP-Seq]

summary: Deep sequencing has revealed that epigenetic modifiers are the most mutated genes in acute myeloid leukemia (AML). Thus, elucidating epigenetic dysregulation in AML is crucial to understand disease mechanisms. Here, we demonstrate that Metal Response Element Binding Transcription Factor 2/Polycomblike 2 (MTF2/PCL2) plays a fundamental role in the Polycomb repressive complex 2 (PRC2) and that its loss elicits an altered epigenetic state underlying refractory AML. Unbiased systems analyses identified the loss of MTF2-PRC2 repression of MDM2 as central to, and therefore a biomarker for, refractory AML. Thus, immature MTF2- deficient CD34+CD38- cells overexpress MDM2, thereby inhibiting p53 that leads to chemoresistance due to defects in cell cycle regulation and apoptosis. Targeting this dysregulated signaling pathway by MTF2 overexpression or MDM2 inhibitors sensitized refractory patient leukemic cells to induction chemotherapeutics and prevented relapse in AML patient-derived xenograft (PDX) mice. Therefore, we have uncovered a direct epigenetic mechanism by which MTF2 functions as a tumor suppressor required for AML chemotherapeutic sensitivity and identified a potential therapeutic strategy to treat refractory AML.

overall_design: Fold change analysis between treatment and control

first: Harinad

middle: B

last: Maganti

middle: L


title: Antisense transcriptional interference mediates tight gene repression in budding yeast

city: Paris cedex 15

first: Alain

last: Jacquier

address: 25-28 rue du docteur roux

department: Génomes & génétique

institute: Institut Pasteur

summary:
Pervasive transcription generates mainly unstable non-coding transcripts. Although a few examples of pervasive antisense have been shown to mediate gene regulation by transcriptional interference, whether pervasive transcription has a general functional role or merely represents transcriptional noise remains to be determined.

In a mutant context that revealed pervasive transcripts, we characterized more than 800 antisenses genome wide and analysed the corresponding sense mRNA behaviour.

We observed that antisense non-coding transcription is commonly found associated with genes tightly repressed during the exponential phase with an opposite level of mRNA and the associated antisense. This suggested that antisense transcription might participate to a tight repression of genes during the exponential phase. We thus specifically interrupted the antisense transcription of a subset of genes, and found that it resulted in a de-repression of the corresponding mRNAs.

We further validated that this repression acts in cis through a transcriptional interference mechanism, which involves several chromatin modification factors. Transcription interference is observed for the first time as a general mean of gene regulation between cellular states.

overall_design: mRNA and 3'RACE of yeast WT and UPF1∆ in stationary and quiescent phase.

first: Alicia

last: Nevers

first: Antonia

last: Doyen

first: Christophe

last: Malabat

first: Bertrand

last: Néron

first: Thomas

last: Kergrohen

first: Gwenael

last: Badis


title: Peripheral blood biomarkers in Friedreich's ataxia

status: Public on Jul 26 2018

city: Los Angeles

first: Daniel

last: Nachun

address: 695 Charles E Young Dr S

institute: UCLA

summary: The identification of biomarkers for Friedreich’s ataxia (FRDA), a rare and debilitating recessive Mendelian neurodegenerative disorder, is an important goal for disease follow-up and assessment of treatments. Clinical scales are not sensitive enough to detect small, short-term changes that may be indicative of treatment effectiveness. We used differential expression, correlation with expansion size, network analysis, machine learning, and enrichment analysis to identify gene expression biomarkers which differentiated FRDA patients from both heterozygous expansion carriers and controls (821 individuals in total), resulting in a disease signature for FRDA. Our 27-gene expression panel  includes genes which are linked to inflammation, lipid metabolism and apoptosis, and overlaps with previous studies and a with a novel mouse model for FRDA. Future studies should seek to expand the search for FRDA biomarkers to include changes in epigenetic regulation and protein expression.

overall_design: 1299 peripheral blood samples, of which 733 were used in study.  4 samples were run twice, but were not intended as technical replicates.  Sample status is indicates by characteristics: sample column and can be either patient, heterozygous carrier or control

first: Giovanni

last: Coppola

first: David

last: Lynch

first: Sue

last: Perlman


title: Identification of differentially expressed genes between control and miR-371~373 cluster-overexpressing colorectal cancer cells

city: Belvaux

first: Elisabeth

last: Letellier

address: 6, Avenue du Swing

department: Life Sciences Research Unit

country: Luxembourg

institute: University of Luxembourg

summary:
The miR-371~373 cluster is a suspected repressor of colon cancer initiation and progression. To better understand its role in metastasis initiation, we used microarray expression analysis to identify potential target genes of this miRNA cluster
Potential target genes were defined as significantly downregulated genes after stable overexpression of the miR-371~373 cluster

overall_design: We performed a stable overexpression of a control vector or a specific miR-371~373 cluster-containing vector in 2 different CRC spheroid cultures. Three technical replicates were used for each condition.


title: Effect of DNA binding small molecules on the genomic distribution of nucleosomes with H3K27Ac

status: Public on Jul 20 2018

first: Katerina

last: Gurova

state: NY

summary: Small molecule CBL0137 destabilizes nucleosome directly via binding to DNA. Effect of CBL0137 on nucleosomes with mark specific for more open chromatin characteristic for promoters and enhancers versus all nucleosomes H3 was measured.

overall_design: HT1080 cells were treated with 3uM of CBL0137 for 6 hours

first: Jianmin

last: Wang