title: Protein acyltransferase DHHC3 regulates breast tumor growth, oxidative stress and senescence.

first: Chandan

last: Sharma

address: 450 Brookline Avenue

department: Cancer Immunology and Virology

institute: Dana Farber Cancer Institute

summary: Protein acyltransferase DHHC3 is upregulated in malignant and metastatic human breast cancer, and its elevated expression correlates with diminished survival not only in human breast cancer but also in six other cancer types. In a direct demonstration of pro-tumor DHHC3 function, ZDHHC3 ablation diminished both MDA-MB-231 mammary cell xenografts growth and the size of metastatic lung colonies. Gene array data and fluorescence dye assays documented increased oxidative stress and senescence in ZDHHC3-ablated cells. Consistent with increased senescence, ZDHHC3-ablated tumors showed enhanced recruitment of innate immune cells (anti-tumor macrophages, NK cells) associated with clearance of senescent tumors. ZDHHC3-ablation effects (decreased tumor growth, increased oxidative stress, increased senescence) were reversed upon reconstitution with wildtype, but not enzyme active site-deficient DHHC3. ZDHHC3-ablation effects on oxidative stress/senescence were also substantially reversed upon concomitant ablation of upregulated oxidative stress driver TXNIP. Diminished DHHC3-dependent palmitoylation of ERGIC3 protein likely plays a key role in TXNIP upregulation. In conclusion, through its palmitoylation activity, DHHC3 supports in vivo breast tumor growth by a mechanism involving negative modulation of tumor cell oxidative stress and senescence.

overall_design: The MDA-MB-231 cells stably ablated for control and DHHC3 protein expression were injected into nude mice (10 injections each with control and D3 ablated cells), and the tumor volumes were assessed over a 30-day period. Subsequently, the mice were sacrificed, followed by excision of tumors. The small portion of the excised tumors were used for RNA extraction and eventually DNA microarray analysis (two replicates each from control and DHHC3 ablated tumors).

first: Martin

last: Hemler


title: Effects of Inhibition of CDK8/19 Mediator Kinase by Senexin A in HEK293 cells treated with TNF-alpha  I

status: Public on Aug 18 2017

city: Columbia

first: Mengqian

last: Chen

state: SC

address: CLS710, 715 Sumter Street

department: College of Pharmacy

country: USA

institute: University of South Carolina

summary: We have investigated the effects of CDK8/19 inhibitor Senexin A on NFκB-mediated transcription, induced by a canonical NFκB activator, TNFα.

overall_design: HEK293 cells were pre-treated with or without 5 μM Senexin A for 1 hour, followed by treatment with or without 10 ng/ml TNFα for 30 minutes.

first: Jiaxin

last: Liang

first: Hao

last: Ji

first: Zhengguan

last: Yang

first: Serena

last: Altilia

first: Bing

last: Hu

first: Adam

last: Schronce

first: Martina

last: McDermott

first: Gary

middle: P

last: Schools

first: Chang-uk

last: Lim

first: David

last: Oliver

first: Michael

middle: S

last: Shtutman

first: Tao

last: Lu

first: George

middle: R

last: Stark

first: Donald

middle: C

last: Porter

first: Eugenia

middle: V

last: Broude

first: Igor

middle: B

last: Roninson


title: Patient-derived hiPSC neurons with heterozygous CNTNAP2 deletions display altered neuronal gene expression and network activity

status: Public on Aug 19 2017

city: New York

first: Erin

middle: K

last: Flaherty

state: New York

address: 1425 Madison Ave

department: Neuroscience

institute: Icahn School of Medicine

type: Expression profiling by high throughput sequencing

summary: We queried the expression of CNTNAP2 in Ngn2-induced neurons from each member of this family trio, hypothesizing that heterozygous intragenic deletions may affect the expression of CNTNAP2.

overall_design: RNA was harvested after 21 days of Ngn2-induction. The New York Genome Center prepared RNAseq libraries using the KAPA Total 350bp kit, followed by 2x125bp Illumina RNA sequencing to a read depth of 40M reads per sample on the HiSeq 2500.

first: Rania

middle: M

last: Deranieh

first: Elena

last: Artimovich

first: Inkyu

last: Lee

first: Arthur

middle: J

last: Siegel

first: Deborah

middle: L

last: Levy

middle: W

last: Nestor

first: Kristen

last: Brennand


title: Expression profiling macrophage subsets

city: St. Louis

first: DAvid

last: DeNardo

state: Mo

address: 660 S. Euclid Ave

department: Medicine

institute: Washington University

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

overall_design: Refer to individual Series


title: The Arabidopsis thaliana wild-type (Ws-2) and CLAVATA1 (clv1.12 and clv1.13) mutant transcriptomes upon the compatible interaction with Hyaloperonospora arabidopsidis

city: Sophia Antipolis

first: Harald

last: Keller

address: 400 route des Chappes

department: UMR-ISA

country: France

institute: INRA

summary: We used Arabidopsis full-genome microarrays to characterize plant transcript accumulations in wild-type plants and clv mutants, 3 days after water treatment and inoculation with the biotrophic oomycete downy mildew pathogen, Hyaloperonospora arabidopsidis.

overall_design: In two independent experiments, cotyledons from the wild-type Wassilewskija (Ws-2) ecotype and from two allelic clv (clv1.12 and clv1.13) mutants were treated with water, or inoculated with the H. arabidopsidis isolate Emwa1 to establish a compatible interaction. Affymetrix ATH1 microarrays were used to profile Arabidopsis transcript accumulations at 3 days after onset of treatment.

first: M

last: Hanemian

first: B

last: Favery

first: Y

last: Marco

first: H


title: Gene expression of anti-TNF induced macrophages

city: Amsterdam

first: Felica

last: Bloemendaal

address: Meibergdreef 69-71

department: Experimental Gastroenterology

country: Netherlands

institute: AMC

summary: Anti-TNF induced macrophages from MLR (6) were compared to IFNγ (6), IL-4 (6) and IL-10 (6) polarized macrophage subsets.

overall_design: PBMC from healthy volunteers were co-cultured in a 1:1 ratio to create a MLR. Anti-TNF (infliximab) was added on day 2 and CD14+ macrophages were isolated on day 7. Monocytes from the same donors were isolated from PBMC on day 0 using Percoll density-gradient centrifugation. Monocytes were then polarized with IFN-γ, IL-4 or IL-10 for 7 days.

first: F

middle: E

last: Wildenberg

first: S

last: Meisner

first: J

last: Lum

first: G

last: van den Brink


title: Linker histone H1 prevents R-loop accumulation and genome instability in heterochromatin

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

country: Spain

institute: IRB Barcelona

type: Genome binding/occupancy profiling by high throughput sequencing


title: microRNA-143/145 loss induces Ras-signaling and cooperates with Pten-deficiency to promote basal-like breast cancer [CGH]

city: Toronto

first: Sharon

last: Wang

state: Ontario

address: 67 College Street Room 456

country: Canada

institute: University of Toronto

summary:
The tumor suppressor PTEN is frequently inactivated in breast and other cancers; yet, germ-line mutations in this gene induce non-malignant hamartomas, indicating dependency on additional cooperating events.  Here we show that most tumors derived from conditional deletion of mouse Pten in mammary epithelium are highly differentiated and lack transplantable tumor initiating cells (TICs) capable of seeding new tumors following orthotopic injection of FACS-sorted or tumorsphere cells. A rare group of poorly differentiated tumors did harbour transplantable TICs. These transplantable tumors exhibited distinct molecular classification, signaling pathways, chromosomal aberrations and mutational landscape, as well as reduced expression of microRNA-143/145. Stable knockdown of miR-143/145 conferred tumorigenic potential upon poorly transplantable Pten-deficient tumor cells through a mechanism involving induction of RAS signaling, leading to increased sensitivity to MEK inhibition. In humans, miR145-deficiency significantly correlated with elevated RAS pathway activity in basal-like breast cancer, and patients with combined PTEN/miR-145 loss or PTEN-loss/RAS pathway activation exhibited poor clinical outcome. These results underscore a selective pressure for combined PTEN loss together with miR-145 loss or high RAS-pathway activity in aggressive forms of breast cancer, and a need to identify and prioritize these tumors for aggressive therapy.
Array CGH data comparing 2 types of Pten-deficient tumors (well and poorly differentiated) with other modles of mouse mammary tumors

overall_design:
2 histological types of Wap-Cre:Ptenfl/fl were compared

Raw data files for GSM2644828, GSM2644834, GSM2644836 and GSM2644837 are incomplete and contain duplicated data rows and have missing data. Please see sample records for description of file errors.

first: Eldad

last: Zacksenhaus


title: Linker histone H1 prevents R-loop accumulation and genome instability in heterochromatin [ChIP Seq]

summary: Genome wide distribution of gammaH2AvD in Wild Type and RNAi dH1 Drosophila melanogaster S2 cells

overall_design: ChIP-Seq peak calling of gammaH2AvD against Input sample in Drosophila melanogaster S2 WT and RNAi dH1 cells

first: Aleix

last: Bayona

first: Anna

last: Casas-Lamesa

last: Reina

first: Jordi

last: Bernués

first: Fernando

last: Azorin


title: Transcriptomic profile in lymphomonocytes of healthy subjects identifies an early signature of insulin resistance and related diseases

city: Parma

first: Eleonora

last: Derlindati

address: via gramsci, 14

country: Italy

institute: University of Parma

summary: Insulin resistance is considered to be a pathogenetic mechanism in several and diverse diseases (e.g. type 2 diabetes, atherosclerosis) often antedating them in apparently healthy subjects. The aim of this study was to investigate whether IR per se is characterized by a specific pattern of gene expression.  We analyzed the transcriptomic profile of peripheral blood mononuclear cells in two groups (10 subjects each) of healthy individuals, with extreme insulin resistance or sensitivity, matched for BMI, age and gender, selected within the MultiKnowledge Study cohort (n=148). Data were analyzed with an ad-hoc rank-based classification method.  321 genes composed the gene set distinguishing the insulin resistant and sensitive groups, within which the “Adrenergic signaling in cardiomyocytes” Kegg pathway was significantly represented, suggesting a pattern of increased intracellular cAMP and Ca2+, and apoptosis in the IR group. The same pathway allow to discriminate between insulin resistance and insulin sensitive subjects with BMI >25,  supporting his role as a biomarker of IR. Moreover, ASCM pathway  harbored biomarkers able to distinguish healthy and diseased subjects (from publicly available data sets) in IR-related diseases involving excitable cells: type 2 diabetes, chronic heart failure, and Alzheimer’s disease.  Altered gene expression profile of the ASCM pathway is an early molecular signature of IR and could provide a common molecular pathogenetic platform for IR-related disorders, possibly representing an important aid in the efforts aiming at preventing, early detecting and optimally treating IR-related diseases.

overall_design: comparison between two groups of 10 subjects each; biomarker has been validated in another population of two groups of 10 subjects each

first: Alice

last: Matone

first: Luca

last: Marchetti

first: Valentina

last: Spigoni

first: Alessandra

last: Dei Cas

first: Barbara

last: Montanini

first: Diego

last: Ardigò

first: Ivana

last: Zavaroni

first: Corrado

last: Priami

first: Riccardo

last: Bonadonna


title: Expression profiling macrophage subsets [P1750]

first: DAvid

last: DeNardo

summary:
Experiments expression profile several FACS-sorted pancreas tumor-associated macrophages.
Tumor-associated macrophages (TAMs) are essential components of the cancer microenvironment and play critical roles in the regulation of tumor progression. Optimal therapeutic intervention requires in-depth understanding of the sources that sustain macrophages in malignant tissues. In this study, we investigated the ontogeny of TAMs in murine pancreatic ductal adenocarcinoma (PDAC) models. We identified both inflammatory monocytes and tissue-resident macrophages as sources of TAMs. Unexpectedly, significant portions of pancreas-resident macrophages originate during embryonic development and expand through in situ proliferation during tumor progression. While monocyte-derived TAMs play more potent roles in antigen presentation, embryonically derived TAMs exhibit a pro-fibrotic transcriptional profile, indicative of their role in producing and remodeling extracellular matrix molecules. Collectively, these findings uncover the heterogeneity of TAM origin and functions, and could provide therapeutic insight for PDAC treatment.

overall_design: Macrophages were either sorted from the normal pancreas or PDAC tissues of wild-type, or KPC or FLT3-CRE/LSL-YFP mice.

first: Yu

last: Zhu

first: Brett

last: Knolhoff

first: David


title: Quantitative analysis of chromatin occupancy (ChIP-Seq) from wild-type mice and Kdm5c KO mice in standard conditions (H3K4me3, H3K4me1, and Kdm5C) or upon novelty exposure (H3K4me3), and control mice and Kdm5c ifKO mice in basal state (H3K4me3).

city: Sant Joan d'Alacant

first: Angel

last: Barco

state: Alicante

address: Av. Santiago Ramón y Cajal

institute: Instituto de Neurociencias (UMH-CSIC)

summary: Chromatin immunoprecipitation (ChIP) experiments were conducted as previously described (Ito et al, 2013) using anti-H3K4me3 (Millipore, #07-473), anti-H3K4me1 (Abcam, #ab8895), or anti-Kdm5C (Iwase et al., 2016). Hippocampi derived from two different animals were pooled together for each sample and two independent biological replicates per condition were sequenced according to manufacturer instructions in a HiSeq2500 apparatus (Illumina, Inc). Information on library preparation method, size of the libraries, and mapping to reference genome can be found in Supplementary Material accompanying the manuscript. ChIP-seq reads were aligned to the mouse genome (Mus_musculus.GRCm.38.83) using bowtie2 (v2.2.9) (Langmead and Salzberg, 2012) and further processed using samtools (v1.3.1) (Li et al., 2009). Peak calling was performed using MACS2 (v2.1.0) (Zhang et al., 2008) with default parameters except for Kdm5c that were as follows: -q 0.01 --nomodel --extsize 131 --broad --broad-cutoff 0.1. Read counts on aligned bam files were performed using Rsubread (v1.22.3) (Liao et al., 2014). Differential peak methylation analysis for H3K4me3 chromatin mark was performed using DESeq2 (v1.10.0) (Love et al., 2014) of the bioconductor suite (Huber et al., 2015) in the R (v3.3) statistical computing platform. For consideration of differentially methylated regions between conditions, we used adjusted p-value < 0.05 as indicated in the manuscript.

overall_design: Genome-wide profiles for H3K4me3, H3K4me1, and Kdm5C from adult mouse hippocampus were generated by deep sequencing, in duplicate, using Illumina HiSeq 2500. Each sample was prepared by pooling hippocampal tissue from 2 idenpendent mice.

first: Jose

last: Lopez-Atalaya

first: M

last: Scandaglia


title: Transcriptome analysis in petals and leaves of chrysanthemums   with different chlorophyll levels

city: Tsukuba

first: Akemi

last: Ohmiya

state: Ibaraki

address: Fujimoto 2-1

department: Institute of Vegetable and Floriculture Science

country: Japan

institute: National Agriculture and Food Research Organization

summary: To identify the regulatory steps that control chlorophyll accumulation, we compared gene expression in petals and leaves of chrysanthemum cultivars with different chlorophyll levels. Microarray analyses showed that the expression levels of chlorophyll biosynthesis genes encoding glutamyl-tRNA reductase, Mg-protoporphyrin IX chelatase, Mg-protoporphyrin IX monomethylester cyclase, and protochlorophyllorophyllide oxidoreductase were well associated with chlorophyll content: their expression levels were lower in white petals than in green petals, and were highest in leaves. Among chlorophyll catabolic genes, expression of STAY-GREEN, encoding Mg-dechelatase, which is a key enzyme controlling chlorophyll degradation, was considerably higher in white and green petals than in leaves. We searched for transcription factor genes whose expression was well related to chlorophyll level in petals and leaves and found several such genes.

overall_design: Expression of white petals (FW, Feeling White), green petals (FG, Feering Green; FGII, Feeling Green Dark), and mature leaves of chrysanthemums was analyzed. The analysis was performed in biological triplicate.

first: Katsutomo

last: Sasaki


title: Consequences of supplying methyl donors during pregnancy on the methylome of the offspring from lactating and non-lactating dairy cattle

status: Public on Aug 17 2017

city: Caldes de Montbui

first: Alex

last: Bach

address: Torre Marimon

department: Ruminant Production

institute: IRTA

type: Methylation profiling by high throughput sequencing

summary: The aim of this study was to evaluate the potential effects of methyl donor supplementation of pregnant animals in the presence or absence of a concomitant lactation on the methylome of the offspring. Twenty Holstein cows, 10 nulliparous (not lactating while pregnant) and 10 multiparous (lactating while pregnant) were blocked by parity and randomly assigned to an i.m. weekly injections of a placebo (CTRL) or a solution containing methyl donors (MET). After calving, 5 calves randomly selected from each treatment (two born to primiparous and three to multiparous dams) were blood-sampled to determine their full methylome. There were more than 2,000 CpG differentially methylated between calves born to CTRL and those born to MET, and also between calves born to multiparous and nulliparous dams. Most of the differences affected genes involved in immune function, cell growth regulation and differentiation, kinase activity, and ion channeling. We conclude that the coexistence of pregnancy and lactation affects the methylome of the offspring, and that supplementation of methyl donors early in gestation has also consequences on the methylome.

overall_design: 10 samples, with 5 replicates for the effect of methyl donors


title: Cyclooxygenase gene (Ptgs) exchange and differentially regulated inflammatory pathways in peritoneal macrophages

city: Kingston

first: Xinzhi

last: Li

address: 18 Stuart Street

department: Biomedical and Molecular Sciences

institute: Queen's University

summary: The aim of the current study was to characterize the differential inflammatory signaling pathway of COX isoforms during systemic inflammation in mice. Peritoneal macrophages from mice challenged with either lipopolysaccharide (2 mg/kg body weight, WT, COX-2>COX-1, COX-1>COX-2, and Reversa mice) or PBS (Control, WT mice) were harvested. RNA (100 ng) was used to determine gene expression changes utilizing pre-built Mouse Inflammation V2 CodeSets to carry out Nanostring analysis. Our results indicate inflammatory networks can be maintained by isoform exchange in inflamed macrophages. However, COX-1>COX-2 macrophages show reduced activation of inflammatory signaling pathways, indicating that COX-1 may be replaced by COX-2 within this complex milieu, but not vice versa.

overall_design: A dose of 2 mg/kg lipopolysaccharide (LPS) (body weight), diluted in sterile PBS, was injected intraperitoneally into WT (annotated as WT+LPS), COX-2>COX-1, COX-1>COX-2, and Reversa mice (12-16 wk; n=6 each group). An equivalent volume of PBS alone was given to another group of WT mice (Control group, annotated as WT-LPS). At 6 h post-injection, peritoneal macrophages were harvested and extracted for RNA analysis.

first: Colin

last: Funk


title: Fragile X Syndrome causes epigenetic disruptions treatable with BET inhibitor Jq1

city: Philadelphia

first: Erica

last: Korb

state: PENNSYLVANIA

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania


title: ChIP-sequencing of histone marks in WT and Fmr1-/- (KO) neurons and mice

summary: Widespread misregulation of histone modifcations occur in FXS, most notably increases in marks associated with active transcription.

overall_design: 7DIV cultured cortical neurons from WT or Fmr1 KO mice were processed for H3K4me3 and H3K27ac ChIP. In addition, neurons sorted from cerebellar tissue from WT and Fmr1 KO BAC-TRAP NeuroD1 P15 mice were used for H3K4me3 ChIP, performed in triplicate


title: Effects of Inhibition of CDK8/19 Mediator Kinase by Senexin A in HEK293 cells treated with TNF-alpha  II

first: Mengqian

last: Chen

overall_design: HEK293 cells were pre-treated with or without 5 μM Senexin A for 1 hour, followed by treatment with or without 10 ng/ml TNFα for different time period.

first: Jiaxin

last: Liang

first: Hao

last: Ji

first: Zhengguan

last: Yang

first: Serena

last: Altilia

first: Bing

last: Hu

first: Adam

last: Schronce

first: Martina

last: McDermott

first: Gary

last: Schools

first: Chang-uk

last: Lim

last: Oliver

first: Michael

last: Shtutman

first: Tao

last: Lu

first: George

last: Stark

first: Donald

last: Porter

first: Eugenia

last: Broude

first: Igor

last: Roninson


title: Genome-wide DNA methylation analysis in blood cells from patients with Werner Syndrome

city: Bologna

first: Maria Giulia

last: Bacalini

address: Via Altura 3

department: Brain Aging Laboratory

institute: IRCCS Istituto delle Scienze Neurologiche di Bologna

summary: Genome wide DNA methylation profiling of whole blood samples from 3 subjects affected by Werner Syndrome and 3 age- and sex- matched controls. The Infinium MethylationEPIC BeadChip was used to obtain DNA methylation profiles across approximately 850,000 CpGs.

overall_design: DNA was bisulfite-converted using the EZDNA Methylation-Gold Kit (Zymo Research) and analysed using the Infinium HumanMethylationEPIC BeadChip (Illumina) following manufacturer's instructions.

first: Tiziana

last: Guastafierro

first: Maria

middle: G

first: Antonella

last: Marcoccia

first: Davide

last: Gentilini

last: Pisoni

first: Anna-Maria

last: Di Blasio

first: Alessandro

last: Corsi

first: Claudio

last: Franceschi

first: Alberto

last: Spanò

first: Domenico

last: Raimondo

first: Paolo

last: Garagnani

first: Francesco

last: Bondanini


title: First critical repressive H3K27me3 marks in embryonic stem cells identified using designed protein inhibitor

city: Seattle

first: Hannele

last: Ruohola-Baker

state: WA

address: 850 Republican Street

institute: Institute for Stem Cell and Regenerative Medicine

summary: The polycomb repressive complex 2 (PRC2) histone methyl-transferase plays a central role in epigenetic regulation in development and in cancer, and hence to interrogate its role in a specific developmental transition, methods are needed for disrupting function of the complex with high temporal and spatial precision. The catalytic and substrate recognition functions of PRC2 are coupled by binding of the N-terminal helix of the Ezh2 methylase to an extended groove on the EED trimethyl lysine binding subunit. Disrupting PRC2 function can in principle be achieved by blocking this single interaction, but there are few approaches for blocking specific protein-protein interactions in living cells and organisms. Here, we describe the computational design of proteins that bind to the EZH2 interaction site on EED with sub-nanomolar affinity in vitro and form tight and specific complexes with EED in living cells. Induction of the EED binding proteins abolishes H3K27 methylation in human embryonic stem cells (hESC) and at all but the earliest stage blocks self-renewal, pinpointing the first critical repressive H3K27me3 marks in development.

overall_design: 1 biological sample were isolated from naïve hESC cell line Elf1 and Elf1 expressing EED binder 22.2. RNA-seq and ChIP-seq (H3K27me3) was performed for each sample.

first: James

middle: D

last: Moody

first: Yuliang

last: Wang


title: Mutant p53 Shapes the Enhancer Landscape of Cancer Cells in Response to Chronic Immune Signaling

city: San Diego

first: Shannon

last: Lauberth

state: California

address: 9500 Gilman Drive #0322, Bonner Hall 3202

department: Biological Sciences

institute: UCSD

summary: We establish a mechanism by which chronic TNF-a signaling orchestrates a functional interplay between mutant p53 and NFkB that underlies altered patterns of cancer promoting gene expression.

overall_design: examination of various histone mark accumulation; mutp53, NFkB, RNAPII binding; and nascent transcription upon chronic TNF signaling in SW480 colon cancer cells

first: Homa

last: Rahnamoun

first: Hanbin

last: Lu

first: Sascha

middle: H

last: Duttke

first: Christopher

last: Benner

last: Glass


title: Culture-induced recurrent epigenetic aberrations in human pluripotent stem cells [methylation]

city: Pardess hana

first: Uri

last: Weissbein

state: Please Select

address: Haalon 4

department: Genetics

country: Israel

institute: Hebrew University of Jerusalem

type: Methylation profiling by genome tiling array

summary: Human pluripotent stem cells (hPSCs) are an important player in disease modeling and regenerative medicine. Nonetheless, multiple studies uncovered their inherent genetic instability upon prolonged culturing, where specific chromosomal aberrations provide cells with a growth advantage. These positively selected modifications have dramatic effects on multiple cellular characteristics. Epigenetic aberrations also possess the potential of changing gene expression and altering cellular functions. In the current study, we assessed the landscape of DNA methylation aberrations during prolonged culturing of hPSCs, and defined a set of genes which are recurrently hypermethylated and silenced. We further focused on one of these genes, testis-specific Y-encoded like protein 5 (TSPYL5), and demonstrated that when silenced, differentiation-related genes and tumor-suppressor genes are downregulated, while pluripotency- and growth-promoting genes are upregulated. This process is similar to the hypermethylation-mediated inactivation of certain genes during tumor development. Our analysis highlights the existence and importance of recurrent epigenetic aberrations in hPSCs during prolonged culturing.

overall_design: Genome-wide DNA methylation profiling by Illumina Infinium HumanMethylation 450K Beadchip was performed on human embryonic stem cells treated with 5-aza-2'-deoxycytidine or control cells.

first: Nissim

last: Benvenisty


title: Next-generation sequencing measuring genome-wide RNA decay by s4U Seq in naïve CD4+ T cells from Mettl3 WT and KO mice

city: New Haven

first: Huabing

last: Li

state: CONNECTICUT

address: 1 Gilbert Street, S570

department: Immunobiology

institute: Yale University School of Medicine

summary: Naïve T cells of Mettl3 KO and WT were pulse labeled by s4U for 15 min before and after IL-7 stimulation for 15min/30min/45min/60min/75min/90min. The total input RNAs or s4U nascent RNAs were isolated and prepared for next-generation sequencing. The RNA response to IL-7 and RNA decay rates were then modeled and calculated, to infer the m6A/Mettl3 effects.

overall_design: Naïve T cells were isolated from Mettl3 KO and WT mice with naïve T cell purification kits (StemCell). The cells were counted and aliquoted 4 million per 1mL FACS buffer per Eppendorf tube. Each tube except t=0 receives 10 µg/ml IL-7 cytokine and incubate in 37℃ incubator. 15 min before spun down and lysed with Trizol, the cells were labeled with 250 µM s4U. The enrichment of s4U-RNA was performed using MTS-biotin chemistry. The input and biotin precipitated RNA were used to prepare library for next-generation sequencing.

first: Richard

last: Flavell

first: Matthew

last: Simon

first: Erin

last: Duffy


title: Comprehensive single cell transcriptional profiling of a multicellular organism by combinatorial indexing

first: Junyue

last: Cao

address: Foege Building S-210, 3720 15th Ave NE

department: Department of Genome Sciences

institute: University of Washington

summary: We developed a combinatorial indexing strategy to profile the transcriptomes of large numbers of single cells or nuclei (Single cell Combinatorial Indexing RNA-seq or sci-RNA-seq). We applied sci-RNA-seq to profile nearly 50,000 cells from C. elegans at the L2 stage, effectively ~56-fold “shotgun cellular coverage” of its somatic cell composition.

sample_organism:
Caenorhabditis elegans
Homo sapiens
Mus musculus

overall_design: human and mouse cell lines, C.elegans.

first: Jonathan

last: Packer

first: Vijay

last: Ramani

first: Darren

middle: A

last: Cusanovich

first: Chau

last: Huynh

first: Riza

last: Daza

first: Xiaojie

last: Qiu

first: Choli

last: Lee

first: Scott

middle: N

last: Furlan

first: Frank

last: Steemers

first: Andrew

last: Adey

first: Robert

last: Waterston

first: Cole

last: Trapnell

first: Jay

last: Shendure


title: m6A mRNA methylation controls T cell homeostasis by targeting IL-7/STAT5/SOCS pathway

first: Huabing

last: Li

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

overall_design: Refer to individual Series


title: Gene expression signatures for hyperoxia in lung cancer cell lines

city: Tokyo

first: Junko

last: Hamamoto

address: 35 Shinanomachi, Shinjuku-ku

department: Pulmonary Medicine

institute: School of Medicine, Keio University

summary: Gene profile of normoxia (20% O2) was compared with that of hyperoxia (50% O2) in lung cancer cell lines.

overall_design: Lung cancer cell lines, H1975 and SK-MES-1 were exposed to 50% O2 for 24h, and total RNA was extracted.


title: Expression data from Arabidopsis root cells

status: Public on Aug 16 2017

city: Shijiahzuang

first: Zhonglin

last: Shang

state: Hebei Province

address: Nanerhuan East Road 20

department: College of Life Sciences

country: China

institute: Hebei Normal University

summary:
Effect of added 0.5 mM ATP on gene expression, 60 min after treatment
We used microarrays to detail ATP-induced up- and down- regulated genes

overall_design: Roots of 4 d-old seedlings were used for RNA extraction and hybridization on Affymetrix microarrays. Gene expression before and after ATP treatment was detected. The relative expression level was calculated.


title: circRNA expression in idiopathic pulmonary fibrosis (IPF) and matched non-fibrotic plasma samples

city: Yan tai

first: Jin

middle: jin

last: Zhang

address: Laishan District

institute: binzhou medical university

summary: We used circRNA microArray analysis from Arraystar to identify differential expression of circRNA in IPF patients compared to healthy controls.

overall_design: The plasmas were distributed into two experimental groups: control group and test group, then perform circRNAs chips by Arraystar Human circRNA Array (8×15 K, Arraystar)

first: Jinjin

first: Changjun

last: Lv


title: Th22 cells represent a distinct human T cell subset involved in epidermal immunity and remodeling

city: Munich

first: Stefanie

last: Eyerich

address: Biedersteinderstrasse 29

country: Germany

institute: Center of Allergy and Environment

summary: Th subsets are defined according to their production of lineage-indicating cytokines and functions. In this study, we have identified a subset of human Th cells that infiltrates the epidermis in individuals with inflammatory skin disorders and is characterized by the secretion of IL-22 and TNF-a, but not IFN-g, IL-4, or IL-17. In analogy to the Th17 subset, cells with this cytokine profile have been named the Th22 subset. Th22 clones derived from patients with psoriasis were stable in culture and exhibited a transcriptome profile clearly separate from those of Th1, Th2, and Th17 cells; it included genes encoding proteins involved in tissue remodeling, such as FGFs, and chemokines involved in angiogenesis and fibrosis. Primary human keratinocytes exposed to Th22 supernatants expressed a transcriptome response profile that included genes involved in innate immune pathways and the induction and modulation of adaptive immunity. These proinflammatory Th22 responses were synergistically dependent on IL-22 and TNF-a. Furthermore, Th22 supernatants enhanced wound healing in an in vitro injury model, which was exclusively dependent on IL-22. In conclusion, the human Th22 subset may represent a separate T cell subset with a distinct identity with respect to gene expression and function, present within the epidermal layer in inflammatory skin diseases. Future strategies directed against the Th22 subset may be of value in chronic inflammatory skin disorders.

overall_design: To identify the gene expression profile of human Th22 cell clones


title: Culture-induced recurrent epigenetic aberrations in human pluripotent stem cells

first: Uri

last: Weissbein


title: Antagonistic activities of Sox2 and Brachyury control the fate choice of neuro-mesodermal progenitors

city: Berlin

first: Frederic

last: Koch

address: Ihnestraße 63-73

department: Developmental Genetics

institute: Max Planck Institute for Molecular Genetics

summary: The spinal cord and mesodermal tissues of the trunk such as the vertebral column and skeletal musculature derive from neuro-mesodermal progenitors (NMPs). Sox2, Brachyury (T) and Tbx6 have been correlated with NMP potency and lineage choice, however, their exact role and interaction in these processes have not been revealed yet. Here we present a global analysis of NMPs and their descending lineages performed on purified cells from E8.5 wild-type and mutant embryos. We show that T, cooperatively with WNT signaling, controls the progenitor state and the switch towards the mesodermal fate. Sox2 acts antagonistically and promotes neural development. Tbx6 reinforces the mesodermal fate choice, represses the progenitor state and confers paraxial fate commitment. Our findings refine previous models and establish new concepts of the molecular principles of mammalian trunk development comprising NMP maintenance, lineage choice and mesoderm formation.

overall_design: Bulk transcriptomes (RNA-Seq) and chromatin accessibility (ATAC-Seq) from T/Sox2 expressing subpopulations isolated during trunk development from wildtype and T knock-out mouse embryos. Data is supplemented by Fluidigm single-cell RNA-Seq for T/Sox2 co-expressing cells from wildtype embryos and a bulk RNA-Seq comparison of wildtype and Tbx6 knock-out mouse embryos. ChIP-Seq for T, Sox2, Tbx6 and beta-catenin has been performed with chromatin from in vitro differentiated neuromesodermal progenitors and presomitic mesoderm.

first: Manuela

last: Scholze

first: Lars

last: Wittler

first: Dennis

last: Schifferl

first: Smita

last: Sudheer

first: Phillip

last: Grote

first: Bernd

last: Timmermann

first: Karol

last: Macura

first: Bernhard

last: Herrmann


title: A protein complex regulates RNA processing of intronic heterochromatin-containing genes in Arabidopsis

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

summary: In several eukaryotic organisms, heterochromatin (HC) in the introns of genes can regulate RNA processing, including polyadenylation, but the mechanism underlying this regulation is poorly understood. By promoting distal polyadenylation, the bromo-adjacent homology (BAH) domain-containing and RNA recognition motif-containing protein ASI1 and the H3K9me2-binding protein EDM2 are required for the expression of functional full-length transcripts of intronic HC-containing genes in Arabidopsis. Here we report that ASI1 and EDM2 form a protein complex in vivo via a bridge protein, ASI1-Immunoprecipitated Protein 1 (AIPP1), which is another RNA recognition motif-containing protein. The complex also may contain the Pol II CTD phosphatase CPL2, the plant homeodomain-containing protein AIPP2, and another BAH domain protein, AIPP3. As is the case with dysfunction of ASI1 and EDM2, dysfunction of AIPP1 impedes the use of distal polyadenylation sites at tested intronic HC-containing genes, such as the histone demethylase gene IBM1, resulting in a lack of functional full-length transcripts. A mutation in AIPP1 causes silencing of the 35S-SUC2 transgene and genome-wide CHG hypermethylation at gene body regions, consistent with the lack of full-length functional IBM1 transcripts in the mutant. Interestingly, compared with asi1, edm2, and aipp1 mutations, mutations in CPL2, AIPP2, and AIPP3 cause the opposite effects on the expression of intronic HC-containing genes and other genes, suggesting that CPL2, AIPP2, and AIPP3 may form a distinct subcomplex. These results advance our understanding of the interplay between heterochromatic epigenetic modifications and RNA processing in higher eukaryotes.

overall_design: MethylC-Seq: 3 samples examined and each sample has two replicates, Col-0, aipp1-1, and aipp1-2; mRNA-Seq: 4 samples examined and each sample has two replicates, Col-0, aipp1-1, asi1-2 and edm2-4.

first: Cheng-Guo

last: Duan

first: Xingang

last: Wang

first: Kai

last: Tang


title: RNAseq in C57Bl6 and congenic Atf3-/- mice

city: London

first: Christopher

last: Pin

address: 800 Commissioners Rd. E

department: Physiology and Pharmacology/Peadiatrics

institute: The University of Western Ontario/CHRI

summary: RNA expression from whole pancreatic tissue was assessed by RNA-seq following 4 hours into cerulein-induced pancreatitis in mice lacking the transcription factor ATF3 or congenic C57Bl6 mice. Three mice were used for each group and sequncing performed by Toronto Genomics Centre.

overall_design: Groups included C57Bl6 and Atf3-/- mice; saline and cerulein treated; 4 hours after initial cerulein injection. Each animal received 4 injections over 4 hours of 50 ug/kg cerulein or saline. Each group consisted of three animals.

first: Kurt

last: Berger


title: Transcriptome analysis of gene expression and single-nucleotide-resolution m6A sites in normal and mettl3 cKO testis samples

city: Beijing

first: Qi

last: Zhou

address: Datun Road, Chaoyang District

institute: Institute of Zoology,CAS


title: Transcriptome analysis of gene expression and single-nucleotide-resolution m6A sites in normal and mettl3 cKO testis samples (CLIP-Seq)

summary: RNA was isolated from control and Mettl3 cKO mouse testes using the TRIzol (Invitrogen) reagent by following the manufactures's instructions. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN (RNA integrity number) of higher than 9. For RNA-seq, approximately 2.5 µg of total RNA was then used for library preparation using a KAPA Stranded mRNA-Seq Kit Illumina® platform (KAPABIOSYSTEMS, KR0960) according to the manufacturer’s protocol.For m6A-miCLIP-seq, 6 ug of mRNA was first fragmented and immunoprecipitated with m6A antibody and thus obtained m6A containing RNA was subjected to cDNA library construction according to previously reported method [Linder et al. 2015; PMID: 26121403].All the libraries were sequenced using HiSeq3000 (Illumina) in paired-read mode, creating reads with a length of 101 bp. Sequencing chemistry v2 (Illumina) was used.

overall_design: Examination of gene expressive levels and m6A sites in control and mettl3 cKO mouse testes

last: Xu

first: Ying

last: Yang

first: Baofa

last: Sun

first: Yusheng

last: Chen

first: Guihai

last: Feng


title: Transcriptome analysis of gene expression and single-nucleotide-resolution m6A sites in normal and mettl3 cKO testis samples (RNA-Seq)


title: Recruitment of Armitage and Yb to a transcript triggers its phased processing into primary piRNAs in Drosophila ovaries

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

country: Switzerland

institute: University of Geneva

type: Non-coding RNA profiling by high throughput sequencing

summary: Small RNAs called PIWI -interacting RNAs (piRNAs) are essential for transposon control and fertility in animals. Primary processing is the small RNA biogenesis pathway that uses long single-stranded RNA precursors to generate millions of individual piRNAs, but the molecular mechanisms that identify a transcript as a precursor are poorly understood. Here we demonstrate that artificial tethering of the piRNA biogenesis factor, Armi, to a transcript is sufficient to direct it into primary processing in Drosophila ovaries and in an ovarian cell culture model. In the fly ovarian somatic follicle cells, the transcript becomes cleaved in a stepwise manner, with a 5ʹ→3ʹ directionality, liberating U1-containing ~24 nt piRNAs that are loaded into Piwi. Although uridines are preferred for generation of piRNA 5ʹ ends, processing takes place even in their absence, albeit at a lower efficiency. We show that recombinant Armi has 5ʹ→3ʹ helicase activity, and mutations that abolish it reduce piRNA processing. Another somatic piRNA pathway factor Yb, and an interactor of Armi, is also able to trigger piRNA biogenesis when tethered to a transcript. Tethering-mediated primary piRNA biogenesis is also functional in the fly ovarian germline and loads all the three PIWI proteins present in this environment. Our study finds a broad correlation between piRNA processing and localization of the tethered factors to the cytoplasmic perinuclear ribonucleoprotein granules called germline nuage or somatic Yb bodies. We conclude that transcripts bound by Armi and Yb are identified as piRNA precursors, resulting in localization to cytoplasmic processing granules and their subsequent engagement by the resident piRNA biogenesis machinery.

overall_design: Different proteins were tested in their ability to trigger piRNA production from the reporter transcript upon their tethering to the transcript.  Transgenic fly lines and ovarian somatic cell (OSC) culture were used. Immunopurified piRNAs were sequenced and those originating from the reporter transcript were identified.

first: Radha

last: Raman Pandey

first: David

last: Homolka

first: Kuan-Ming

first: Ravi

last: Sachidanandam

first: Marie-Odile

last: Fauvarque

middle: S


title: Elucidating the role of UCP1 and FGF21 for metabolic homeostasis in the cold

city: Garching

first: Martin

last: Jastroch

address: Parkring 13

department: Institute for Diabetes and Obesity

institute: Helmholtz Zentrum München

summary: Global RNA sequencing  analysis of the hypothalamus, BAT, inguinal WAT and muscle of long-term cold exposed WT, FGF21 KO, UCP1 KO and UCP1/FGF21 double KO mice

overall_design: The experiment was performed in homozygous, male WT, FGF21 KO, UCP1 KO and UCP1/FGF12 double KO (dKO) mice. All mice were bred, born and weaned at 30°C. At the age of 10 to 12 weeks, mice were transferred to a temperature-controlled (+/- 0.5°C) climate chamber and kept for 12 days at 18°C followed by 3 weeks at 5°C. Afterwards, mice were euthanized after 2-3 hours food withdrawal, and serum and tissue samples were collected.

first: Susanne

last: Keipert


title: Analysis of Ribosome Protected Fragments of mRNAs from yeast strains either expressing Rio1p or depleted of Rio1p

city: Toulouse

first: Beata

last: Jady

address: 118 route de Narbonne

institute: Laboratoire de Biologie Moléculaire Eucaryote

summary: mRNAs bound by ribosomes from yeast cells were analysed in order to determine the exact position of ribosomes in the presence or absence of Rio1p. Beside total Ribosome Protected Fragments (RPFs), RPFs from mRNAs protected by immature pre-40S pre-ribosomes was also analysed. The analysis showed that immature 40S ribosomes can carry out translation and their premature entry into translation is hindered by Rio1p.

overall_design: mRNAs fragments protected by ribosomes were subjected to NGS Ribosome Profiling experiment. Samples included (1) total ribosome-associated mRNAs from yeast cells expressing Rio1p, (2) total ribosome-associated mRNAs from yeast cells depleted of Rio1p and (3) immuno-selected mRNAs associated with immature pre-40S pre-ribosomal particles from yeast-cells depleted of Rio1p. Ribosome-protected mRNA fragments were used as templates for cDNA libraries. The resulting cDNAs were sequenced and the sequences were annealed to the yeast genome. The position of the reads were determined in relation to either the translation start site or the stop codon of the corresponding coding DNA sequences.

first: Kamila

last: Belhabich-Baumas

first: Clément

last: Joret

first: Beáta

last: Jády

first: Célia

last: Plisson-Chastang

first: Ramtin

last: Shayan

first: Christophe

last: Klopp

first: Anthony

last: Henras

first: Yves

last: Henry

first: Annie

last: Mougin


title: Expression data from functional studies using RNAi on Lamin B1 in BL2 cells

city: Ulm

first: Johannes

last: Bloehdorn

address: Albert-Einstein-Allee 23

institute: University of Ulm

summary:
Lamin B1 is a component of the nuclear envelope involved in epigenetic chromatin regulation and is reduced during B cell activation and formation of lymphoid germinal centres. RNAi-mediated reduction of Lamin B1 results in spontaneous SHM as well as kappa-light chain aberrant surface expression showing that Lamin B1 is a negative epigenetic regulator of SHM.
We used Affymetrix Exon 1.0 ST microarrays to detail the global programme of gene expression underlying changes induced in siRNA-treated Lamin B1low BL2 cells. siRNA-mediated reduction of nuclear Lamin B1 incorporation resulted in a general upregulation of positive cell cycle regulatory genes which in turn occurred alongside an upregulation of genes responsible for cell cycle checkpoint execution or cell cycle arrest, and were specific for LMNB1 reduction.

overall_design: Gene expression profiling on BL2 cell line was conducted for 2 independently cultured passages with 4 experimental approaches each, with 1) control with non-targeting siRNA 2) control with non-targeting siRNA and after induction of SHM 3) LMNB1 RNAi transfected 4) LMNB1 RNAi transfected and after induction of SHM. For siRNA treated samples, SMARTpool LMNB1 siRNA mixture of three siRNAs in equimolar concentration was used.

first: Andrejs

last: Braun

first: Tetyana

last: Klymenko


title: N6-Methyladenosine Guides mRNA Alternative Translation during Integrated Stress Response

status: Public on Aug 15 2017

city: Hangzhou

first: Yuanhui

last: Mao

state: Zhejiang

address: 1369 West Wenyi Road

institute: Zhejiang University

summary: The integrated stress response (ISR) facilitates cellular adaptation to a variety of stress conditions via phosphorylation of the common target eIF2α. During ISR, the translation of certain stress-related mRNAs is upregulated in spite of global suppression of protein synthesis.The selective translation often relieson alternative mechanisms, such as leaky scanning or reinitiation, but the underlying mechanism remains incompletely understood. Here we report that,in response to amino acid starvation, the reinitiation of ATF4 is not only governed by eIF2α-controlled ternary complex availability, but is also subjected to regulation by mRNA methylation in the form of N6-methyladenosine (m6A). We demonstrate that m6A in the 5' untranslated region (5’ UTR) controls ribosome scanning and subsequent start codonselection. Global profiling of initiating ribosomes reveals widespread alternative translation events influenced by mRNA methylation. Consistently, Fto-transgenic mice manifest enhanced ATF4 expression, highlighting the critical role of 5’ UTR methylation in translational regulation of ISR at cellular and organismal levels.

overall_design: Ribo-seq, QTI-seq and m6A-seq in Scramble, ALKBH5 knockdown and FTO overexpression

first: Ji

last: Wan

first: Jun

last: Zhou

first: Shu-Bing

last: Qian


title: Regulatory DNA in A. thaliana can tolerate high levels of sequence divergence

city: Seattle

first: Christine

last: Queitsch

address: 3720 15th Ave NE

department: Genome Sciences

summary: Variation in regulatory DNA is thought to drive evolution. Cross-species comparisons of regulatory DNA have provided evidence for both weak purifying selection and substantial turnover in regulatory regions. However, disruption of transcription factor binding sites can affect the expression of neighboring genes. Thus, the base-pair level functional annotation of regulatory DNA has proven challenging. Here, we explore regulatory DNA variation and its functional consequences in genetically diverse strains of the plant Arabidopsis thaliana, which largely maintain the positional homology of regulatory DNA. Using chromatin accessibility to delineate regulatory DNA genome-wide, we find that 15% of approximately 50,000 regulatory sites varied in accessibility among strains. Some of these accessibility differences are associated with extensive underlying sequence variation, encompassing many deletions and dramatically hypervariable sequence. For the majority of such regulatory sites, nearby gene expression was similar, despite this large genetic variation. However, among all regulatory sites, those with both high levels of sequence variation and differential chromatin accessibility are the most likely to reside near genes with differential expression among strains. Unexpectedly, the vast majority of regulatory sites that differed in chromatin accessibility among strains show little variation in the underlying DNA sequence, implicating variation in upstream regulators.

overall_design: Regions of varying chromatin accessibility were compared across strains of A. thaliana; This series contains RNA-seq data for Col-0 seedlings that were treated with auxin, grown in darkness or control.

first: Kerry

last: Bubb


title: Transcriptomic analysis of Lysinibacillus varians reveal the genetic foundation of its cell cycle

city: Guangzhou

first: chunjie

last: zhu

state: Guangdong

address: 100 xianlie road, yuexiu district

institute: Guangdong Institute of Microbiology

summary: Lysinibacillus varians GY32 was isolated from river sediment of electronic waste recycling site. Its invariably filament-to-rod cell cycle represents a novel bacteria morphogenesis that is crucial in understanding cell division coordination with lifecycle and environmental bacteria adaptation. A description of genes and biological processes involved in the special filament-to-rod cell cycle of L. varians GY32 is within reach.

overall_design: As a representative of filament cell and rod cell, 5 h and 10 h culture of strain GY32 were used to transcriptome sequencing

first: Chunjie

last: Zhu

first: Guoping

last: Sun

last: Guo

first: Meiying

last: Xu


title: The RNA Uridyltransferase Zcchc6 is expressed in macrophages and impacts innate immune responses

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary: Alveolar macrophages orchestrate pulmonary innate immunity and are essential for early immune surveillance and clearance of microorganisms in the airways. Inflammatory signaling must be sufficiently robust to promote host defense but limited enough to prevent excessive tissue injury. Macrophages in the lungs utilize multiple transcriptional and post-transcriptional mechanisms of inflammatory gene expression to delicately balance the elaboration of immune mediators. RNA terminal uridyltransferases (TUTs), including the closely homologous family members Zcchc6 (TUT7) and Zcchc11 (TUT4), have been implicated in the post-transcriptional regulation of inflammation from studies conducted in vitro. In vivo, we observed that Zcchc6 is expressed in mouse and human primary macrophages. Zcchc6-deficient mice are viable and born in Mendelian ratios and do not exhibit an observable spontaneous phenotype under basal conditions. Following an intratracheal challenge with S. pneumoniae, Zcchc6 deficiency led to a modest but significant increase in the expression of select cytokines including IL-6, CXCL1, and CXCL5. These findings were recapitulated in vitro whereby Zcchc6-deficient macrophages exhibited similar increases in cytokine expression due to bacterial stimulation. Although loss of Zcchc6 also led to increased neutrophil emigration to the airways during pneumonia, these responses were not sufficient to impact host defense against infection.

overall_design: Alveolar macrophages isolated from wild-type and Zcchc6-/- animals were profiled using whole-genome gene expression microarrays.

first: Elyse

last: Kozlowski

first: Matt

last: Jones


title: Whole-genome resequencing of T-DNA insertion lines

city: Heidelberg

first: Quentin

last: Gouil

state: VIC

address: Studley Road

country: Australia

institute: Olivia Newton-John Cancer Research Institute

summary: Whole-genome resequencing of eight transcription factor mutants and one wild-type, in order to verify the T-DNA insertion site and its uniqueness.

overall_design: Nextera whole-genome library and paired-end sequencing, to find the T-DNA insertion site(s)

first: Reena

last: Narsai


title: COORDINATED REGULATION OF THE EIIMAN AND FRURKI OPERONS OF STREPTOCOCCUS MUTANS BY GLOBAL AND FRUCTOSE-SPECIFIC PATHWAYS

status: Public on Aug 14 2017

city: Gainesville

first: Robert

last: Burne

state: Florida

address: 1395 Center Drive

department: Oral BIology

institute: University of Florida

summary: The glucose/mannose-PTS permease EIIMan encoded by manLMN in the dental caries pathogen Streptococcus mutans has a dominant influence on sugar-specific, CcpA-independent catabolite repression (CR). Mutations in manL affect energy metabolism and virulence-associated traits, including biofilm formation, acid tolerance and competence. Using promoter:reporter fusions, expression of the manLMN and the fruRKI operons, encoding a transcriptional regulator, a fructose-1-P kinase and a fructose-PTS permease EIIFru, respectively, was monitored in response to carbohydrate source and in mutants lacking CcpA, FruR, and components of EIIMan. Expression of genes for EIIMan and EIIFru was directly regulated by CcpA and CR, as evinced by in vivo and in vitro methods. Unexpectedly, not only was the fruRKI operon negatively regulated by FruR, but so was manLMN. Carbohydrate transport by EIIMan had a negative influence on expression of manLMN, but not fruRKI. In agreement with the proposed role of FruR in regulating these PTS operons, loss of fruR or fruK substantially altered growth on a number of carbohydrates, including fructose. RNA deep sequencing revealed profound changes in gene regulation caused by deletion of fruK or fruR. Collectively, these findings demonstrate intimate interconnection of the regulation of two major PTS permeases in S. mutans and reveal novel and important contributions of fructose metabolism to global regulation of gene expression.

overall_design: mRNA profiling of the wild type UA159 and two mutants fruK-13 and fruR, each grown to exponential phase in batch on a rich medium BHI.

first: Lin

last: Zeng

first: Brinta

last: Chakraborty

first: Tanaz

last: Farivar


title: Genomic analysis of Tet2 knockout macrophages

city: New Haven

first: Jun

last: Lu

state: CT

address: 10 Amistad St.

department: Yale Stem Cell Center

institute: Yale University

summary: Ten-Eleven-Translocation-2 (Tet2) is a DNA methylcytosine dioxygenase that functions as a tumor suppressor in hematopoietic malignancies. In this study, we revealed a role for Tet2 in sustaining the immunosuppressive function of tumor-tissue myeloid cells.  We found that Tet2 expression is increased in intratumoral myeloid cells both in mouse models of melanoma and in melanoma patients, and that this increased expression is dependent on an IL-1R-MyD88 pathway. Ablation of Tet2 in myeloid cells suppressed melanoma growth in vivo, and shifted the immunosuppressive gene expression program in tumor-associated macrophages to a proinflammatory one, with a concomitant reduction of the immunosuppressive function. This resulted in increased numbers of effector T cells in the tumor, and T cell depletion abolished the reduced tumor growth observed upon myeloid-specific deletion of Tet2. Our findings reveal a non-cell-intrinsic, tumor-promoting function for Tet2, and suggest that Tet2 may present a therapeutic target for the treatment of non-hematologic malignancies.

overall_design:
[BMDM] This dataset contains RNAseq experiments of in vitro polarized bone marrow derived macrophages (BMDMs), with wildtype (WT) or Tet2 knockout (KO) genotype.
For BMDM experiments, BMDMs were differentiated from WT or Tet2 KO mice, and were treated with IL4 (20 ng/ml) for 0, 10 or 24 hours. Cells were harvested for RNA for RNAseq with two biological replicates.

[5hmC] This dataset contains DNA-immunoprecipitation sequencing (DIP-seq) experiments of  genome-wide 5-hydroxymethylcytosine (5hmC) levels in wildtype (WT) or Tet2 knockout (KO) bone marrow derived macrophages (BMDMs).
For 5hmC experiments, BMDMs were differentiated from WT or Tet2 KO mice, and were treated with IL4 (20 ng/ml) for  24 hours. Genomic DNA was harvested and 5hmc binding DNA segments was pulled down by 5hmc specific antibody for DIP-seq.

[TAM] This dataset contains RNAseq experiments of tumor associated macrophages (TAMs) isolated from wildtype (WT) or Myeloid-specific Tet2 knockout (KO) mice .
For TAM experiments, YUMM1.7 cell line  was injected into WT (LysMcre wt/wt, Tet2 fl/fl) or Tet2 KO mice (LysMcre +/wt, Tet2 fl/fl). TAMs were harvested from the resultant tumors for RNAseq analysis.

first: Wen

last: Pan


title: methylC-seq, RNA-seq and sRNA-seq data over Arabidopsis thaliana germination

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

overall_design: Refer to individual Series


title: Immunoprofiling of CD14+ blood monocytes upon Zika virus infection

city: Los Angeles

first: Suan-Sin

last: Foo

address: 1501 San Pablo St

department: Molecular Microbiology and Immunology

institute: University of Southern California

summary: Blood CD14+ monocytes are the frontline immunomodulators categorized into classical, intermediate or non-classical subsets, subsequently differentiating into M1 pro- or M2 anti-inflammatory macrophages upon stimulation. While Zika virus (ZIKV) rapidly establishes viremia, the target cells and immune responses, particularly during pregnancy, remain elusive. Furthermore, it is unknown whether African- and Asian-lineage ZIKV have different phenotypic impacts on host immune responses. Using human blood infection, we identified CD14+ monocytes as the primary target for African- or Asian-lineage ZIKV infection. When immunoprofiles of human blood infected with ZIKV were compared, a classical/intermediate monocyte-mediated M1-skewed inflammation by African-lineage ZIKV infection was observed, in contrast to a non-classical monocyte-mediated M2-skewed immunosuppression by Asian-lineage ZIKV infection. Importantly, infection of pregnant women’s blood revealed enhanced susceptibility to ZIKV infection. Specifically, Asian-lineage ZIKV infection of pregnant women’s blood led to an exacerbated M2-skewed immunosuppression of non-classical monocytes in conjunction with global suppression of type I interferon-signaling pathway and an aberrant expression of host genes associated with pregnancy complications. 30 ZIKV+ sera from symptomatic pregnant patients also showed elevated levels of M2-skewed immunosuppressive cytokines and pregnancy complication-associated fibronectin-1. This study demonstrates the differential immunomodulatory responses of blood monocytes, particularly during pregnancy, upon infection with different lineages of ZIKV.

overall_design: Whole blood infection was performed with African ZIKV (MR766) and Asian ZIKV (H/PF/2013), followed by pan monocyte isolation at 40 hours post infection (hpi). Isolated monocytes were lysed in RLT buffer at a concentration of 6500 cells/ul. A volume of 1.5 ul of cell lysate per specimen was used for NanoString nCounter assay using Human Myeloid Panel (650 genes).

first: Suan


title: Gene expression response to altered gravity, simulated gravity and hypergravity in human T cells

city: Zurich

first: Cora

middle: S.

last: Thiel

address: Winterthurerstrasse 190

department: Institute of Anatomy

institute: University of Zurich


title: MITF and BRN2 contribute to metastatic growth after dissemination of melanoma.

city: Brisbane

first: Glen

last: Boyle

state: Queensland

address: 300 Herston Road Herston

department: Department of Cell and Molecular Biology, Cancer Program

institute: QIMR Berghofer Medical Research Insitute

summary: Melanoma tumors are highly heterogeneous, comprising of different cell types that vary in their potential for growth and invasion.  Heterogeneous expression of the Microphthalmia-associated Transcription Factor (MITF) and the POU domain transcription factor BRN2 (POU3F2) has been found in malignant melanoma.  Changing expression of these transcription factors as the disease progresses has been linked to the metastatic mechanism of phenotype switching.  We therefore investigated the effects of MITF and BRN2 expression in melanoma growth and metastasis.  Depletion of MITF resulted in a cell population that had a slowed cell cycle progression, was less invasive in vitro and had hindered tumor and metastasis forming ability in mouse xenograft studies.  BRN2 depletion left a cell population with intact proliferation and invasion in vitro; however metastatic growth was significantly reduced in the mouse xenograft model.  These results suggest that the proliferative population within melanoma tumors express MITF, and both MITF and BRN2 are important for metastatic growth in vivo.  This finding highlights the importance of BRN2 and MITF expression in development of melanoma metastasis.

overall_design: Single colour, Illumina Human HT12v4 Beadarrays.

first: Jacinta

last: Simmons

first: Carly

last: Pierce

first: Fares

last: Al-Ejeh


title: rahu is a mutant allele of Dnmt3c, encoding a DNA methyltransferase homolog required for meiosis and transposon repression in the mouse male germline [WGBS]

city: New York

first: Cem

last: Meydan

state: New York

address: 1305 York

department: Physiology & Biophysics

institute: Weill Cornell Medical College

summary: Transcriptional silencing by heritable cytosine-5 methylation is an ancient strategy to repress transposable elements. It was previously thought that mammals possess four DNA methyltransferase paralogs—Dnmt1, Dnmt3a, Dnmt3b and Dnmt3l—that establish and maintain cytosine-5 methylation. Here we identify a fifth paralog, Dnmt3c, that is essential for retrotransposon methylation and repression in the mouse male germline. From a phenotype-based forward genetics screen, we isolated a mutant mouse called ‘rahu’, which displays severe defects in double-strand-break repair and homologous chromosome synapsis during male meiosis, resulting in sterility. rahu is an allele of a transcription unit (Gm14490, renamed Dnmt3c) that was previously mis-annotated as a Dnmt3-family pseudogene. Dnmt3c encodes a cytosine methyltransferase homolog, and Dnmt3crahu mutants harbor a non-synonymous mutation of a conserved residue within one of its cytosine methyltransferase motifs, similar to a mutation in human DNMT3B observed in patients with immunodeficiency, centromeric instability and facial anomalies syndrome. The rahu mutation lies at a potential dimerization interface and near the potential DNA binding interface, suggesting that it compromises protein-protein and/or protein-DNA interactions required for normal DNMT3C function in vivo. Dnmt3crahu mutant males fail to establish normal methylation within LINE and LTR retrotransposon sequences in the germline and accumulate higher levels of transposon-derived transcripts and proteins, particularly from distinct L1 and ERVK retrotransposon families. Phylogenetic analysis indicates that Dnmt3c arose during rodent evolution by tandem duplication of Dnmt3b, after the divergence of the Dipodoidea and Muroidea superfamilies. These findings provide insight into the evolutionary dynamics and functional specialization of the transposon suppression machinery critical for mammalian sexual reproduction and epigenetic regulation.

overall_design: Six samples total: Dnmt3c+/+ (three biological replicates) and Dnmt3crahu/rahu (three biological replicates) mice aged 12 days post partum

first: Devanshi

last: Jain

first: Julian

last: Lange

first: Corentin

middle: C

last: Bouuaert

first: Christopher

last: Mason

first: Kathryn

last: Anderson

first: Scott

last: Keeney


title: NFIA Controls the Brown Fat Gene Program by Co-Localizing with PPARgamma at Cell-Type-Specific Enhancers

city: Tokyo

first: Hironori

last: Waki

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

institute: The University of Tokyo


title: rahu is a mutant allele of Dnmt3c, encoding a DNA methyltransferase homolog required for meiosis and transposon repression in the mouse male germline


title: Glycomic gene comparison between human epidermal melanocytes and human metastatic melanoma cells

status: Public on Aug 13 2017

city: La Jolla

first: Steven

last: Head

state: CA

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

summary: To discover potential biomarkers of melanoma development and progression, we embarked on studies comparing the glycomic gene profiles of normal human epidermal melanocytes with human metastatic melanoma (MM) cells represented by A375 and G361 cell lines.  Glycomic features embody all of those enzymatic, membranous and regulatory proteins that influence glycan ‘sugar’ formation/degradation on a cell.  Comparative expression profiling of glycomic genes indicated that several genes were differentially expressed between normal melanocytes and MM cells.  We speculate that glycome genes differentially expressed in MM cells help drive malignant and metastatic behavior of MM cells and could potentially serve as a biomarker(s) of melanoma progression.

overall_design: Comparative gene expression analysis was performed on (2) samples of normal human epidermal melanocytes and on (2) samples each of human metastatic melanoma A375 and G361 cell lines.

first: Jenna

last: Geddes-Sweeney

first: Jennifer

last: Liang

first: Kang

last: Shuli

middle: R

first: Charles

last: Dimitroff


title: DOCK8 enforces immunological tolerance by promoting IL-2 signaling and immune synapse formation in Treg cells

status: Public on Aug 12 2017

city: Cambridge

first: Erin

last: Janssen

address: 15 Chalk St

department: Medicine

institute: Boston Children's Hospital

summary: Patients deficient in the guanine nucleotide exchange factor DOCK8 have decreased numbers and impaired in vitro function of T regulatory (Treg) cells and make autoantibodies, but seldom develop autoimmunity. We show that similarly, Dock8-/- mice have decreased numbers and impaired in vitrofunction of Treg cells, but do not develop autoimmunity. In contrast, mice with selective DOCK8 deficiency in Treg cells develop lymphoproliferation, autoantibodies, and gastrointestinal inflammation, despite normal percentage and in vitro function of Treg cells, suggesting that deficient T effector cell function might protect DOCK8 deficient patients from autoimmunity. We demonstrate that DOCK8 associates with STAT5 and is important for IL-2 driven STAT5 phosphorylation in Treg cells. DOCK8 localizes within the lamellar actin ring of the Treg cell immune synapse (IS). Dock8-/- Treg cells have abnormal TCR-driven actin dynamics, decreased adhesiveness, altered gene expression profile, an unstable IS with decreased recruitment of signaling molecules, and impaired transendocytosis of the co-stimulatory molecule CD86. These data suggest that DOCK8 enforces immunological tolerance by promoting IL-2 signaling, TCR-driven actin dynamics, and the IS in Treg cells.

overall_design: CD4+CD25+CD39+YFP+ and CD4+CD25+CD39+YFP‑ Treg cells were isolated from the spleen and lymph nodes of Foxp3YFP-Cre/+/Dock8flox/flox mice.  Treg cells were then cultured overnight in complete media alone or in the presence of media + anti-CD3+CD28 beads (1 bead per cell). After 16 hours, cells were harvested and the RNA was isolated. For unstimulated samples, there were 4 independent YFP- samples and 6 independent YFP+ samples.  For bead stimulated samples, there were 3 independent YFP- samples and 2 YFP+ samples.

first: Victor

last: Barrera


title: NFIA Controls the Brown Fat Gene Program by Co-Localizing with PPARgamma at Cell-Type-Specific Enhancers (chromatin)

summary: Brown fat dissipates energy as heat and protects against obesity. Here, we identified nuclear factor I-A (NFIA) as a novel transcriptional regulator of brown fat by a genome-wide open chromatin analysis of murine brown and white fat followed by motif analysis of brown-fat-specific open chromatin regions. NFIA and the adipogenic master regulator, PPARgamma, co-localize at the brown-fat-specific enhancers. Moreover, the binding of NFIA precedes and facilitates the binding of PPARgamma, leading to increased chromatin accessibility and active transcription. Introduction of NFIA into myoblasts results in brown adipocyte differentiation. Conversely, the brown fat of NFIA knockout mice displays impaired expression of the brown-fat-specific genes and reciprocal elevation of muscle genes. Finally, expression of NFIA and the brown-fat-specific genes is positively correlated in human brown fat. These results indicate that NFIA is a key transcriptional regulator of brown fat and exerts its effects by co-localizing with PPARg at cell-type-specific enhancers.

overall_design: FAIRE-seq analysis of murine BAT, iWAT and eWAT, ChIP-seq analysis in immortalized brown adipocytes and NFIA-expressing C2C12 myoblasts, and ATAC-seq analysis in immortalized brown adipocytes.

first: Yuta

last: Hiraike

first: Masahiro

last: Nakamura

first: Ken

last: Suzuki

first: Ryo

last: Nakaki

first: Shogo

last: Yamamoto

first: Shuichi

last: Tsutsumi

first: Hiroyuki

last: Aburatani

first: Toshimasa

last: Yamauchi

first: Takashi

last: Kadowaki


title: Single-cell mass cytometry reveals the impact of graphene nanomaterials with human primary immune cells

city: Sassari

first: Lucia

middle: Gemma

last: Delogu

address: Via Muroni 23

department: Chemistry and Pharmacy

institute: University of Sassari

summary: The genome-wide transcriptome analysis highlight the increased biocompatibility on immune cells of graphene functionalized with amino groups (NH2) compared with graphene oxide (GO); reducing the cell metabolism disfunction. Moreover, GONH2 was found to polarizes T-cell and monocyte activation toward a T helper-1/M1 immune response.

overall_design: Total RNA obtained from isolated T cells (Jurkat) and Monocytes (THP1) cell lines incubated with graphenes (conc 50µg/mL) for 24 hours compared to untreated control cells.

first: Marco

last: Orecchioni

first: Davide

last: Bedognetti

first: Leon

last: Newman

first: Claudia

last: Fuoco

first: Filomena

last: Spada

first: Wouter

last: Hendrickx

first: Francesco

last: Marincola

last: Sgarrella

first: Filipe

last: Rodrigues

first: Cécilia

last: Ménard-Moyon

first: Gianni

last: Cesareni

first: Kostas

last: Kostarelos

first: Alberto

last: Bianco


title: DNA Methylation-dependent regulation of Cathepsin E gene expression by the transcription factor Kaiso in MRL/lpr mice.

city: Okayama

first: Jun

last: Wada

address: 2-5-1 Shikata-cho, Kita-ku

department: Department of Nephrology, Rheumatology, Endocrinology and Metabolism

institute: Okayama University

summary: Global DNA hypomethylation in CD4+ cells in SLE patients was suggested to play a key role in the pathogenesis. To identify new methylation-sensitive genes, we integrated genome-wide DNA methylation and mRNA profiling in CD4+ cells of MRL/lpr (MRL) and C57BL6/J (B6) mice. We identified Ctse, in which 13 methyl-CpGs within 583 bp region of intron 1 were hypomethylated, and mRNA upregulated in MRL compared with B6 mice. One of methyl-CpGs, mCGCG was hypomethylated and mutated to CGGG in MRL mice. Kaiso is known to bind mCGCG and we hypothesized that it represses expression of Ctse. The binding of Kaiso to mCGCG site in B6 was reduced in MRL mice revealed by ChIP-PCR. EL4 cells treated with 5-azaC and/or TSA showed the suppression of the binding of Kaiso to mCGCG motif and the overexpression of Ctse was demonstrated by qPCR. Ctse gene silencing by siRNA in EL4 cells resulted in reduction of IL-10 secretion. Accordingly, IL10 and CTSE mRNAs up-regulated in CD4+ T cells both in MRL mice and the patients with SLE. The hypomethylation of mCGCG motif, reduced recruitment of Kaiso, and increased expression of Ctse and Il-10 in CD4+ cells may be involved in the pathogenesis of SLE.

overall_design: To identify new candidate genes regulated by DNA methylation and involved in the pathogenesis of systemic lupus erythematosus (SLE), we performed Illumina Hiseq to analyze the genome-wide DNA methylation and expression of mRNA of CD4+ T cell isolated from spleens in MRL/lpr-Tnfrsf6lpr  (MRL) mice and C57BL/6J (B6) mice. Both mice are female, 16 weeks old. For Illumina analysis, we used one mouse of MRL mice and one mouse of B6 mice.

first: Sumie

last: Hiramatsu


title: LncRNA expression profiling for 9 human plasma samples from systemic lupus erythematosus patients and healthy controls

city: Hefei, Anhui

first: Guo-Cui

last: Wu

address: 81 Meishan Road

department: Department of Epidemiology and Biostatistics, School of Public Health

institute: Anhui Medical University

summary: To screen the differentially expressed lncRNAs, we performed lncRNA profiling using ArrayStar Human LncRNA Microarray in 24 new-onset systemic lupus erythematosus (SLE) patients and 12 age- and sex-matched healthy controls (HCs). For the lncRNA microarray screening, total RNA from plasma was isolated from 12 SLE without nephritis, 12 lupus nephritis (LN) and 12 HCs. Four RNA samples were mixed togther as a pool of sample for microarray analysis. Accordingly, there were each three pooled RNA samples from 12 SLE without nephritis, 12 LN and 12 HCs for microarray analysis. Hierarchical clustering showed the plasma levels of lncRNAs and mRNAs differed significantly between 24 new-onset SLE patients and 12 control subjects. With a fold change ≥ 2 and P ≤ 0.05, we identified 1315 significantly differentially expressed lncRNAs (743 lncRNAs up-regulated and 572 lncRNAs down-regulated) and 1363 differentially expressed mRNAs (745 mRNAs up-regulated and 618 mRNAs down-regulated) in plasma of SLE patients compared with control samples.

overall_design: The human LncRNA microarray analysis of the 9 plasma samples from systemic lupus erythematosus patients and healthy controls

first: Hai-Feng

last: Pan

first: Dong-Qing

last: Ye


title: Salmonella Typhimurium ATCC14028 fimZ mutant

city: Taipei

first: Chang

last: Chieh-Hsiang

address: No. 1, Sec. 4, Roosevelt Rd

country: Taiwan

institute: National Taiwan University

summary: Fimbriae are hair-like structures present on the outer membrane of many Enterobacteriaceae and such appendages are proposed to play a significant role in the attachment of the bacteria to host cells and tissues. Salmonella enterica serovar Typhimurium has the potential to produce 13 different fimbrial types, among which type 1 fimbriae is the most common found. Expression of type 1 fimbriae is cooperatively controlled by fimZ, fimY, stm0551, fimW, and fimU within the fim gene cluster. FimZ belongs to the response regulator of the two-component regulatory system in bacteria and functions as a DNA binding protein. FimZ is a positive regulator for type 1 fimbrial expression in S. Typhimurium. A fimZ mutant in ATCC 14028 strain constructed by allelic exchange did not produce type 1 fimbriae. Total RNA was extracted from the parental ATCC 14028 and its fimZ mutant cultured in static broth and analyzed by hybridization to a S. Typhimurium LT2 DNA microarray. Transcriptomic analysis indicated that the type 1 fimbriae related genes, multidrug efflux protein gene acrF were down-regulated, whereas flagella associated genes, chemotaxis and virulence genes such as invF and invH genes were up-regulated in the fimZ mutant strain. It is possible that FimZ protein may play a role to interact with other genes besides regulating type 1 fimbriae.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

overall_design: RNA transcript of Salmonella Typhimurium ATCC14028 strain comparing wild-type with fimZ mutant. Two-cindition experiment, wild-type vs. fimZ mutant strain.

first: K

last: Yeh

first: C

last: Chang


title: Transcriptome data of Penicillium citrinum regulated by pH

city: Zhenjiang

first: Xiangfeng

last: Zheng

state: Jiangsu

address: 301, Xuefu Road

department: Food school

institute: Jiangsu university

summary: Penicillium citrinum X9-4, which was isolated from infected grapes by our laboratory, produced the highest amount of OTA at pH 5 in culture media, and toxin-production was restrained under acidic environment (pH 3). It revealed the possible mechanism of OTA biosynthesis and metabolic regulation in P. citrinum by transcriptomics, and investigated the reason of OTA biosynthesis was restrained in P. citrinum when cultured under acidic environment.

overall_design: Penicillium citrinum cultured at pH 3 (control, non OTA production) and pH 5 (produce highest amount of OTA)

first: Hongyin

last: Zhang

first: Lina

last: Zhao


title: Transcriptome-based network analysis reveals renal cell type-specific dysregulation of hypoxia-associated transcripts [glomeruli]

city: Ann Arbor

first: Jennifer

last: Harder

state: Michigan

address: 1150 W. Medical Center Drive

department: Division of Nephrology

institute: The University of Michigan

summary: Accumulating evidence suggests that dysregulation of hypoxia-regulated transcriptional mechanisms is involved in development of chronic kidney diseases (CKD). However, it remains unclear how hypoxia-induced transcription factors (HIFs) and subsequent biological processes contribute to CKD development and progression. In our study, genome-wide expression profiles of more than 200 renal biopsies from patients with different CKD stages revealed significant correlation of HIF-target genes with eGFR in glomeruli and tubulointerstitium. These correlations were positive and negative and in part compartment-specific. Microarrays of proximal tubular cells and podocytes with stable HIF1α and/or HIF2α suppression displayed cell type-specific HIF1/HIF2-dependencies as well as dysregulation of several pathways. WGCNA analysis identified gene sets that were highly coregulated within modules. Characterization of the modules revealed common as well as cell group- and condition-specific pathways, GO-Terms and transcription factors. Gene expression analysis of the hypoxia-interconnected pathways in patients with different CKD stages revealed an increased dysregulation with loss of renal function. In conclusion, our data clearly point to a compartment- and cell type-specific dysregulation of hypoxia-associated gene transcripts and might help to improve the understanding of hypoxia, HIF dysregulation, and transcriptional program response in CKD.

overall_design: Kidney biopsies were microdissected and hybridized on Affymetrix HGU133A and HGU133 Plus 2 arrays. The expression data was normalized  using RMA and CustomCDF v 18 ENTREZG in batches, as indicated. Batch correction was performed using ComBat in GenePattern. The disease groups are Diabetic Nephropathy (DN, n=14), Focal and Segmental Glomerulosclerosis (FSGS, n=22), Focal and Segmental Glomerulosclerosis and Minimal Change Disease (FSGS&MCD, n=6), Hypertensive Nephropathy (HT, n=15), IgA Nephropathy (IgA, n=26), Minimal Change Disease (MCD, n=13), Membranous Glomerulonephritis (MGN, n=21), Rapidly Progressive Glomerulonephritis (RPGN, n=23), Systemic Lupus Erythematosus (SLE, n=30), Thin Membrane Disease (TMD, n=3), and Tumor Nephrectomies (TN, n=14). This dataset has substantial overlap with GEO datasets  GSE47184,GSE35489, GSE37463

first: Natallia

last: Shved

first: Gregor

last: Warsow

first: Felix

last: Eichinger

first: David

last: Hoogewijs

first: Simone

last: Brandt

first: Peter

last: Wild

first: Matthias

last: Kretzler

first: Clemens

last: Cohen

first: Maja

middle: T

last: Lindenmeyer


title: Transcriptome-based network analysis reveals renal cell type-specific dysregulation of hypoxia-associated transcripts [HK2]

overall_design: Immortalized human podocytes (AB81) and human proximal tubular epithelial cells (HK2) with stable HIF1 and/or HIF2 suppression were subjected to normoxia (N, 20 % O2) or hypoxia (H, 1% O2) for 24h and gene expression profiles were generated. 3 replicates per group


title: Transcriptome-based network analysis reveals renal cell type-specific dysregulation of hypoxia-associated transcripts


title: Expression data from Caco-2 cells infected with F. nucleatum

city: chongqing

first: bin

last: tang

state: chongqing

address: Southwest Hospital &College of Medical Laboratory Science; Third Military Medical University

department: Department of Clinical Microbiology and Immunology

summary:
Caco-2 cells were infected with F. nucleatum (MOI=100:1) or non-infected (control) for 24 hours. Total RNA of cells was extracted using the TRIzol® Reagent (Life Technologies) and cDNA was generated using the PimeScript TMRT Reagent Kit (Takara).
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process.

overall_design: Affymetrix’ new GeneChip® Human Transcriptome Array 2.0 chips were used to analysis 10 specimens (5 F. nucleatum infection, 5 control).

first: Bin

last: Tang


title: Genome-wide identification of Grainy head targets in Drosophila

city: Stockholm

first: Christos

last: Samakovlis

address: Svante Arrhenius väg 20C

department: Department of Molecular Biosciences

country: Sweden

institute: Stockholm University


title: Expression data from calvaria of 10-day-old 13del-tg transgenic mice displaying bone overgrowth.

city: Hong Kong

first: Kwok Yeung

last: Tsang

address: 21 Sassoon Road, Pokfulam

department: School of Biomedical Sciences

country: Hong Kong

institute: The University of Hong Kong

summary:
The ectopic expression of a Col10a1-13del transgene in osteocytes induced ER stress, compromising their differentiation and expression of Sclerostin, resulting in generalized bone overgrowth resembling human crainodiaphyseal chondrodysplasia (CCD).
To elucidate the underlying mechanism of the phenotype, we employed global gene expression profiling analysis.

overall_design: Calvaria bones from 10-day-old (P10) 13del-tg and wild type control littermates (n=3 for each genotype) were obtained for total RNA extraction and hybridization to microarray chips.

first: Kwok

first: Wilson

last: Chan

first: Danny


title: Genome-wide identification of Grainy head targets in Drosophila [gene expression]

summary: Grainy head (Grh) is a conserved transcription factor (TF) controlling epithelial differentiation and regeneration. To elucidate Grh functions, we identified embryonic Grh targets by ChIP-seq and gene expression analysis. We show that Grh controls hundreds of target genes. Repression or activation correlates with the distance of Grh binding sites to the transcription start sites of its targets. Analysis of 54 Grh-responsive enhancers during development and upon wounding suggests cooperation with distinct TFs in different contexts. In the airways, Grh repressed genes encode key TFs involved in branching and cell differentiation. Reduction of the POU-domain TF, Vvl, (ventral veins lacking) largely ameliorates the airway morphogenesis defects of grh mutants. Vvl and Grh proteins additionally interact with each other and regulate a set of common enhancers during epithelial morphogenesis. We conclude that Grh and Vvl participate in a regulatory network controlling epithelial maturation.

overall_design: To investige the effect of the Grainy head (Grh) transcription factor, Drosophila embryos with the following genotypes were subjected to microarray analysis: wild type, grh mutant and grh overexpression. Experiments were carried out in duplicate, and the mutant and overexpression strains were compared to the wild type.

first: Liqun

last: Yao

first: Shenqiu

last: Wang

first: Jakub

middle: O

last: Westholm


title: MED12cKO heart ventricles from male mice

status: Public on Aug 11 2017

city: Dallas

first: Kedryn

middle: K

last: Baskin

state: TX

address: 6000 Harry Hines

department: Molecular Biology

institute: UT Southwestern

overall_design: Refer to individual Series


title: MED12cKO heart ventricles from male mice [ChIP-seq]

summary: The Mediator complex regulates gene transcription by linking basal transcriptional machinery with DNA-bound transcription factors. The activity of the Mediator complex is mainly controlled by a kinase submodule that is comprised of four proteins, including MED12. Although ubiquitously expressed, Mediator subunits can differentially regulate gene expression in a tissue-specific manner. Here, we report that MED12 is required for normal cardiac function such that mice with conditional cardiac-specific deletion of MED12 display progressive dilated cardiomyopathy. Loss of MED12 perturbs expression of calcium handling genes in the heart, consequently altering calcium cycling in cardiomyocytes and disrupting cardiac electrical activity. We identified transcription factors that regulate expression of calcium-handling genes that are downregulated in the heart in the absence of MED12, and found that MED12 localizes to transcription factor consensus sequences within calcium handling genes. We showed that MED12 interacts with one such transcription factor, MEF2, in cardiomyocytes, and that MED12 and MEF2 co-occupy promoters of calcium handling genes. Furthermore, we demonstrated that MED12 enhances MEF2 transcriptional activity and overexpression of both increases expression of calcium handling genes in cardiomyocytes. Our data support a role for MED12 as a coordinator of transcription through MEF2 and other transcription factors. We conclude that MED12 is a regulator of a network of calcium handling genes, consequently “mediating” contractility in the mammalian heart.

overall_design: Ventricle Chipseq profiles of 8wk old control (CTL, CreNEG) and cardiac-specific Med12 knockout mice (Med12cKO, CrePOS) were generated by deep sequencing using seq 2500 v3.

first: Ye

last: Wenduo

first: Eric

last: Olson


title: Arabidopsis buds: dyt1 vs Col; tdf1 vs Col; ams vs Col; ms188 vs Col

city: Shanghai

first: Zhong-Nan

last: Yang

address: Shanghai Guilin Road No.100

institute: Shanghai Normal University

summary: Transcriptional profiling of Arabidopsis buds comparing dyt1, tdf1, ams, ms188 mutants with wild type (Col ecotype), respectively. Goal was to determine the differential expression genes between the buds of mutant and wild type.

overall_design: Biological replicates: 3 replicates of mutant buds, 3 replicates of wildtype buds.

first: Jun

last: Zhu


title: Microarray expression profile of circular RNAs in lung tissues from rats with lipopolysaccharide-induced acute respiratory distress syndrome

city: Changsha

first: Qiquan

last: Wan

address: No 138 Tongzipo Road

institute: Central South University

summary: Acute respiratory distress syndrome (ARDS) remains a common and devastating syndrome. CircRNAs are crucial in a variety of diseases and can provide new potential diagnostic and therapeutic targets for disease. The development of circular RNA (circRNA) microarray has facilitated the study of the role of circRNAs in regulating gene expression. This research was designed to explore the expression profile of circRNAs in lung tissues from rats with lipopolysaccharide-induced ARDS. Our findings indicate that the expression profiles of circRNAs has changed in ARDS as compared with normal rat lung tissue, and may provide novel insight into the molecular mechanism underlying the disease and potential novel diagnostic or therapeutic targets for ARDS.

overall_design: Microarray expression profiling of circRNAs were conducted using RNA extracted from three ARDS rat lung samples and three normal rat lung tissue samples.

first: Wan

last: Qiquan

first: Wu

last: Di

last: Qifa


title: Role of DRH1 in C. elegans virus infection gene expression response

middle: Alexander

last: Miska

address: Tennis Court Road

department: Gurdon Institute

country: United Kingdom

institute: University of Cambridge

summary: Microarray analysis of gene expression changes induced by infection in N2, drh1 and JU1580 (wild strain of C. elegans carrying a deletion of drh1) and JU1580 containing a functional drh-1 as a transgene

overall_design: Comparison of gene expression with and without virus infection

first: Peter

last: Sarkies


title: Transcriptome-based network analysis reveals renal cell type-specific dysregulation of hypoxia-associated transcripts [Tub-FE]

first: Jennifer

last: Harder

overall_design: Kidney biopsies were microdissected and hybridized on Affymetrix HGU133A and HGU133 Plus 2 arrays. The expression data was normalized  using RMA and CustomCDF v 18 ENTREZG in batches, as indicated. Batch correction was performed using ComBat in GenePattern. The disease groups are Cadaveric Donors (CD, n=4), Diabetic Nephropathy (DN, n=18), Focal and Segmental Glomerulosclerosis (FSGS, n=12), Focal and Segmental Glomerulosclerosis and Minimal Change Disease (FSGS&MCD, n=4), Hypertensive Nephropathy (HT, n=20), IgA Nephropathy (IgA, n=24), Minimal Change Disease (MCD, n=12), Membranous Glomerulonephritis (MGN, n=18), Rapidly Progressive Glomerulonephritis (RPGN, n=21), Systemic Lupus Erythematosus (SLE, n=30), Thin Membrane Disease (TMD, n=6), and Tumor Nephrectomies (TN, n=6). This dataset has substantial overlap with GEO datasets  GSE47184,GSE35489, GSE37463

first: Natallia

last: Shved

first: Gregor

last: Warsow

first: Felix

last: Eichinger

first: David

last: Hoogewijs

first: Simone

last: Brandt

last: Wild

first: Matthias

last: Kretzler

first: Clemens

last: Cohen

first: Maja

last: Lindenmeyer


title: Transcriptome-based network analysis reveals renal cell type-specific dysregulation of hypoxia-associated transcripts [AB81]

overall_design: Immortalized human podocytes (AB81) and human proximal tubular epithelial cells (HK2) with stable HIF1 and/or HIF2 suppression were subjected to normoxia (N, 20 % O2) or hypoxia (H, 1% O2) for 24h and gene expression profiles were generated. 3 replicates per group.


title: Modulation of reversibility by DNA Methyltransferases during hepatogenic differentiation in Mesenchymal Stromal Cells

first: Chien-Wei

last: Lee

address: No.155, Sec.2, Linong Street

institute: National Yang-Ming University

summary: Mesenchymal stromal cells (MSCs) hold great promise in the field of liver regenerative medicine. However, the mechanisms and reversibility of hepatogenic differentiation in MSCs are poorly understood. Here, we demonstrate that hepatogenic differentiation of MSCs is a reversible process and is modulated by the transforming growth factor beta 1- DNA methyltransferases (TGF-β1-Dnmts) axis. Dnmt1 and Dnmt3a differentially regulate hepatogenic differentiation and de-differentiation in response to the alternation of TGF-β1 concentration. Knockdown of Dnmt1 accelerates the hepatogenic differentiation in MSCs-derived hepatocyte-like cells (dHeps) whereas Knockdown of Dnmt3a represses hepatogenic differentiation. Conclusions: Our finding first demonstrates that epigenetic regulation by Dnmts in response to stimulation from the surrounding microenvironment controls the reversibility of hepatogenic differentiation in MSCs. Manipulation of Dnmts provides a rapid and efficient differentiation protocol to generate functional dHeps from MSCs that may provide clinical potential for regenerative medicine.

overall_design: Gene expression analysis of hepatogenic differentiation: MSC samples, HD28 samples, dHD28 samples, MLC samples and Hepatocyte samples.

first: Wei-Chih

last: Huang

first: Hsien-Da

first: Yi-Hsiang

last: Ho

first: Muh-Hwa

last: Yang

first: Oscar

first: Vincent


title: Mouse gene expression in wild-type Th17 cells and Pten deficient Th17 cells

status: Public on Aug 10 2017

city: Seoul

first: Gap Ryol

address: 35 Baekbeom-ro, Mapo-gu

department: Department of Life Science

country: South Korea

institute: Sogang University

summary:
Transcriptional profiling of mouse Th17 cells comparing WT Th17 cells with Pten-deficient Th17 cells. Naïve CD4 T cells from each mice were cultured Th17 polarizing condition for 3 days.
Goal was to determine the effects of Pten on global gene expression.

overall_design: Naïve CD4 T cells from WT and Pten KO mice were cultured in Th17 polarizing condition for 3 days, After polarization, total RNA was extracted for affymatrix microarray analysis.

first: G


title: Toxoplasma gondii hexokinase gene knock out mutant expression data

city: Pune

first: Dhanasekaran

last: Shanmugam

state: Maharashtra

address: Dr. Homi Bhabha Road

department: Biochemical Sciences Division

country: India

institute: CSIR-National Chemical Laboratory

summary:
Mutant T. gondii parasites lacking the hexokinase gene were viable. We carried genome wide expression analysis to identify genes that are differentially expressed in the mutant parasite with reference to wild type parental line.
For this microarray analysis, we used the Affymetrix Toxoplasma gondii Custom GeneChip (CDF: ToxoDB version 5); Further details for this array can be found in the GEO platform ID GPL10000

overall_design: Wild type and Tghk mutant parasites were allowed to infect and proliferate within human foreskin fibroblast cells for 48 hours. Total RNA isolated from freshly harvested parasites were further processed by standard protocols for analysis by affymetrix microarray (gene expression data).

last: Roos


title: Posttranscriptional upregulation of HER3 by HER2 mRNA induces Trastuzumab Resistance in breast cancer

city: Beijing

first: Songdong

last: Meng

address: NO.1 Beichen West Road, Chaoyang District

institute: nstitute Of Microbiology Chinese Academy of Sciences

summary: To explore HER2 3’-UTR-dependent transcriptional programs, we analyzed gene-expression profiles of T47D cells transfected with HER2 3’-UTR.

overall_design: Comparative microarray analysis of mRNA for T47D cells transfected with pCDNA3.1-HER2 3’-UTR and pCDNA3.1 as a control was performed on Agilent Whole Human Genome Microarray.

first: Xin

last: Li


title: Loss of a mammalian circular RNA locus causes miRNA deregulation and affects brain function [rRNA-depleted RNA-Seq]

city: Berlin

first: Petar

last: Glazar

address: Robert Rössle Str. 10 (H. 87)

department: Systems Biology of Gene Regulatory Elements

institute: Max Delbrück Center for Molecular Medicine

summary: Hundreds of circular RNAs (circRNAs) are highly abundant in the mammalian brain, often with conserved expression. Here we show that the circRNA Cdr1as is massively bound by the microRNAs (miRNAs) miR-7 and miR-671 in human and mouse brains. When the Cdr1as locus was removed from the mouse genome, knockout animals displayed impaired sensorimotor gating-a deficit in the ability to filter out unnecessary information-which is associated with neuropsychiatric disorders. Electrophysiological recordings revealed dysfunctional synaptic transmission. Expression of miR-7 and miR-671 was specifically and posttranscriptionally misregulated in all brain regions analyzed. Expression of immediate early genes such as Fos, a direct miR-7 target, was enhanced in Cdr1as-deficient brains, providing a possible molecular link to the behavioral phenotype. Our data indicate an in vivo loss-of-function circRNA phenotype and suggest that interactions between Cdr1as and miRNAs are important for normal brain function.

overall_design: We performed rRNA-depleted total RNA sequencing for three knockout and three wild type replicates in four brain regins - cerebellum, cortex, hippocampus and olfactory bulb.

first: Monika

last: Piwecka

last: Glažar

first: Luis

last: Hernandez-Miranda

first: Sebastian

last: Memczak

first: Andrei

last: Filipchyk

first: Filippos

last: Klironomos

first: Luisa

last: Schreyer

first: Salah

last: Ayoub

first: Ralf

last: Kühn

first: Christine

last: Kocks

first: Carmen

last: Birchmeier

first: Nikolaus

last: Rajewsky


title: SRF modulates seizure occurrence, activity induced gene transcription and hippocampal circuit reorganization in the mouse pilocarpine epilepsy model

city: Ulm

first: Bernd

last: Knoell

address: Albert-Einstein Allee 11

institute: Ulm University

summary: The transcription factor SRF (serum response factor) mediates epilepsy mediated gene expression

overall_design: Seizures were induced by administration of pilocarpine, a muscarinic cholinergic agonist [50, 51]. In brief, 20 minutes before pilocarpine administration, animals were injected with a low dose of the cholinergic antagonist methyl scopolamine nitrate (1 mg/kg, s.c.; Sigma, Germany) to reduce peripheral cholinergic effects. Animals received an intra-peritoneal injection of pilocarpine hydrochloride (335 or 350 mg/kg; Sigma, Germany) to induce an SE. Littermate control mice were injected with Ringer solution. Diazepam (4 mg/kg, s.c.; Ratiopharm, Germany) was administered to the animals 40 min after the onset of SE to terminate seizures. All drugs were dissolved in Ringer solution. 100 ng total RNA was used as starting material and 5.5 µg ssDNA per hybridization (GeneChip Fluidics Station 450; Affymetrix, Santa Clara, CA). The total RNAs were amplified and labeled following the Whole Transcript (WT) Sense Target Labeling Assay (http://www.affymetrix.com). Labeled ssDNA was hybridized to Mouse Gene 1.0 ST Affymetrix GeneChip arrays (Affymetrix, Santa Clara, CA). The chips were scanned with an Affymetrix GeneChip Scanner 3000 and subsequent images analyzed using Affymetrix® Expression Console™ Software (Affymetrix). Raw feature data were normalized and intensity expression summary values for each probe set were calculated using robust multiarray average [53]. Microarrays were analyzed with microarray Я US and Limma 2way Anova with p-Value and FDR cutoffs at 0.001 and 2 fold change cut-off.

first: Pascal

last: Lösing

last: Knöll