title: O-GlcNAc transferase recognizes protein substrates using an asparagine ladder in the TPR superhelix

status: Public on Feb 26 2018

city: Boston

first: Suzanne

last: Walker

address: 4 Blackfan Circle

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary:
Abstract: The essential mammalian enzyme O-GlcNAc Transferase (OGT) is uniquely responsible for transferring N-acetylglucosamine to over a thousand nuclear and cytoplasmic proteins, yet there is no known consensus sequence and it remains unclear how OGT recognizes its substrates. To address this question, we have developed a protein microarray assay that chemoenzymatically labels de novo sites of glycosylation with biotin, allowing us to simultaneously as-sess OGT activity across >6000 human proteins. We used this assay to examine the contribution of a conserved asparagine ladder within the lumen of OGT’s superhelical tetratri-copeptide repeat (TPR) domain to substrate selection. When these residues were mutated, OGT retained full activity against short peptides, but showed low to no activity against most of the OGT substrates on the microarray. O-GlcNAcylation of protein substrates in cell extracts was also greatly attenuated. We conclude that OGT recognizes a majority of its substrates by binding them to the asparagine ladder in the TPR lumen proximal to the catalytic domain.
This series contains microarray data both comparing the new chemoenzymatic method to antibody-based detection as well as comparing arrays treated with wild-type OGT, 5N5A mutant OGT, or controls not treated with enzyme. Note: all CTD-stained arrays or control array raw files are contained in GSE107911_RAW.tar

overall_design:
In this study, Invitrogen's Human ProtoArray protein microarray was used as a platform for high-throughput enzyme activity profiling. Multiple batches of microarrays were used over the course of the study, thus the platform represents a composite of the proteins on all microarray batches. Two microarrays were treated with or without OGT and O-GlcNAc was detected by the antibody CTD110.6, 8 microarrays were treated with wild-type OGT and UDP-GlcNAz, followed by chemical labeling with biotin, 7 microarrays were treated with UDP-GlcNAz and biotin but no enzyme as controls, and 3 microarrays were treated with UDP-GlcNAz and an OGT mutant dubbed 5N5A, followed by biotinylation. Individual arrays and treatments are described below in samples

Please note that raw data files associated with multiple analyses/sample records are available as Series supplementary file and are indicated in the corresponding sample description field.

first: Zebulon

middle: G

last: Levine

first: Chenguang

last: Fan

first: Michael

middle: S

last: Melicher

first: Marina

last: Orman

first: Tania

last: Benjamin


title: Gene expression profiling in murine granulocyte-monocyte progenitors (GMP), common dendritic cell progenitors (CDP), committed precursors of classical dendritic cells (pre-cDC), Ly6C+ monocytes (Mo), CD4+ cDC, CD8+ cDC, and neutrophils (Neu)

status: Public on Feb 18 2018

city: Yokohama

first: Tomohiko

last: Tamura

address: 3-9 Fukuura, Kanazawa-ku

department: Department of Immunology

country: Japan

institute: Yokohama City University

summary: To understand the mechanism underlying Mo and DC development

overall_design: Murine GMP, CDP, pre-cDC, Ly6C+ Mo, CD4+ cDC, CD8+ cDC and Neu were isolated from wild-type or IRF8-deficient mice.

first: Daisuke

last: Kurotaki

first: Akira

last: Nishiyama


title: Spine patterning is guided by segmentation of the notochord sheath

status: Public on Feb 20 2018

city: Durham

first: Michel

last: Bagnat

state: North Carolina

address: 333B Nanaline Duke Bldg

department: Cell Biology

country: USA

institute: Duke University

type: Expression profiling by high throughput sequencing

summary: Notochord sheath cells were FACS isolated from 13 days post fertilization (dpf) transgenic zebrafish. Three biological replicates were used for each population, and expression profiles were determined using Illumina HiSeq. Comparison of the sample groups allowed for identification of unique candidates. The sequence reads that passed quality filters were analyzed using HISAT2, and gene counts were analyzed using HTSeq.

overall_design: 3 distinct samples, with 3 replicates each. 3 distinct samples: col9a2+, entpd5a+, and col9a2/entpd5a+ (double) were isolated from the notochord sheath cells of 13 dpf transgenic zebrafish.

first: Susan

last: Wopat


title: Gene expression data from RT112 following FGFR3 knock-down using FGFR3 siRNAs

status: Public on Feb 16 2018

city: paris

first: Elodie

last: chapeaublanc

address: 26 rue d'ulm

department: UMR 144

country: France

institute: Institut Curie

summary: To better understand the molecular mechanisms underlying altered-FGFR3 oncogenic activity in bladder carcinomas, we made use of  RT112 cell lines, which were derived from a human bladder tumor and endogenously expressed the FGFR3-TACC3 fusion protein, the growth and transformation of these cell lines being dependent on activated-FGFR3 activity. We conducted a gene expression analysis using Affymetrix DNA arrays in this cell line treated or not with FGFR3 siRNAs.

overall_design: RT112 cells were transfected or not  with siRNA FGFR3. mRNA was extracted after 40h and gene expression analysis was assessed using the HG-U133 Plus 2.0 array (Affymetrix) array

first: Florent

last: Dufour

first: Damien

last: Plassard

last: Chapeaublanc

first: Isabelle

last: Bernard-Pierrot

first: David

last: Gentien


title: FGFR3 knock-down

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

overall_design: Refer to individual Series


title: Definition of global transcriptional variation in wild type Pseudomonas fluorescens Pf0-1 and its phosphorothioate modification (PT) deficient mutant by RNA-seq analysis

status: Public on Feb 15 2018

city: Wuhan

first: Lianrong

last: Wang

address: Bayi Road

country: China

institute: Wuhan University

summary: To determine whether PT modifications are involved in the epigenetic control of specific genes, RNA-seq analysis was conducted to define global transcriptional changes in early log-phase cultures of wild-type pf0-1 and the PT modifacation related genes(dndBCDE) deletion mutant TT-5. Compared with wild-type pf0-1, a total of ten genes in TT-5 exhibited differential expression of greater than 2-fold (log2-ratio>1 or <-1, p-value<0.05, FDR≤0.001), including 6 up-regulated genes and 4 down-regulated genes (Table 1). Compared with pf0-1, the most significantly downregulated genes were dndBCDE themselves due to the in-frame deletion in TT-5. Of the 6 up-regulated genes, two are phage-related proteins (Pfl01_1169 and Pfl01_3496); the rest are genes encoding a putative membrane protein (Pfl01_0900), xanthine dehydrogenase (Pfl01_1797), N-acetylmuramoyl-L-alanine amidase (Pfl01_5657) and a hypothetical protein (Pfl01_2488). The transcription levels of the differentially expressed genes varied to different degrees and the genes belong to different COG groups.

overall_design: Examination of global transcriptional variation in wild type P. fluorescens Pf0-1 and its phosphorothioate modification (PT) deficient mutant

first: Tong

last: Tong

first: Si

last: Chen


title: Gene expression data from MGH-U3 following FGFR3 knock-down using FGFR3 siRNAs

summary: To better understand the molecular mechanisms underlying altered-FGFR3 oncogenic activity in bladder carcinomas, we made use of  MGH-U3 cell lines, which were derived from a human bladder tumor and endogenously expressed a mutated activated form of FGFR3 (FGFR3-Y375C), the growth and transformation of these cell lines being dependent on activated-FGFR3 activity. We conducted a gene expression analysis using Affymetrix DNA arrays in this cell line treated or not with FGFR3 siRNAs.

overall_design: MGH-U3 cells were transfected or not  with siRNA FGFR3. mRNA was extracted after 72h and gene expression analysis was assessed using the  Human Exon 1.0 ST (Affymetrix) array


title: Effects of in utero and lactational exposure to new generation green plasticizers on adult male rats: a comparative study with di(2-ethylhexyl) phthalate

status: Public on Feb 14 2018

city: Montreal

first: Oceane

last: Albert

state: Quebec

address: 3655 Promenade Sir William Osler, McIntyre Medical Sciences Bldg, Room 107

department: Pharmacology & Therapeutics

country: Canada

institute: McGill University

summary:
Di(2-ethylhexyl) phthalate (DEHP), a widely used plasticizer, is a ubiquitous environmental pollutant and may act as an endocrine disruptor. Early life exposures to DEHP may result in anti-androgenic effects, impairing the development of the male reproductive tract. However, data on the long-lasting consequences of such DEHP exposures on adult male reproductive function are still rare and discrepant. Previously, we identified two novel plasticizers, 1,4 butanediol dibenzoate (BDB) and dioctyl succinate (DOS), as potential substitutes for DEHP that did not reproduce classically described endocrine disrupting phenotypes in prepubertal male offspring after maternal exposure. Here, we investigated the consequences of in utero and lactational exposure to BDB and DOS on adult male rat reproductive function in a comparative study with DEHP and a commercially available alternative plasticizer, 1,2-cyclohexane dicarboxylic acid diisononyl ester (DINCH). Timed pregnant Sprague-Dawley rats were gavaged with vehicle or a test chemical (30 or 300 mg/kg/day) from gestation day 8 to postnatal day 21. While DEHP exposure (300 mg/kg/day) significantly increased epididymal weight in the adult, exposure to DINCH, BDB or DOS did not affect reproductive organ weights, steroid levels or sperm quality. Using a toxicogenomic microarray approach, we found that adult testicular gene expression was affected by exposure to the higher dose of DEHP; transcripts such as Nr5a2, Ltf or Runx2 were significantly downregulated, suggesting that DEHP was targeting estrogen signaling. Lesser effects were observed after treatment with either DINCH or BDB. DOS exposure did not produce such effects, confirming its potential as a responsible substitute for DEHP.
The data deposited correspond to testicular gene expression in 90 day-old Sprague-Dawley rats after exposure to CORN OIL and 30 or 300 mg/kg/day DEHP, DINCH, BDB or DOS from gestational day 8 to post-natal day 21

overall_design: For each of the 9 treatment groups (CORN OIL, DEHP 30, DEHP 300, DINCH 30, DINCH 300, BDB 30, BDB 300, DOS 30, DOS 300), RNA was extracted from the testes of 6 animals from independent litters

first: Océane

first: Thomas

middle: N

last: Nardelli

first: Claudia

last: Lalancette

first: Barbara

middle: F

last: Hales

first: Bernard

last: Robaire


title: RNA Sequencing Analysis to evaluate essential oil dietary supplementation effects in lamb liver and muscle transcriptome

city: Kongens Lyngby

first: Haja

last: Kadarmideen

address: Richard Petersens Plads, Building 324

department: Department of Applied Mathematics and Computer Science

country: Denmark

institute: Technical University of Denmark

summary: Purpose:  The aim of this study was to evaluate the effect of essentail oil dietary supplementation on gene expression in liver and muscle tissue.

overall_design: A total of 32 RNA samples, 16 for muscle and for liver (8 control and 8 treatment) were sequenced on two lanes of Illumina HiSeq 1500 platform generating 101 base-paired end reads.

first: Marcella

last: Sabino

first: Victor

last: Okstoft Carmelo

first: Gianluca

last: Mazzoni

first: Katia

last: Cappelli

first: Stefano

last: Capomaccio

first: Paolo

last: Ajmone-Marsan

first: Andrea

last: Verini-Supplizi

first: Massimo

last: Trabalza-Marinucci


title: Identification of miRNA expression profile CD3+T lymphocytes

city: Lisbon

first: Francisco

middle: J.

last: Enguita

address: Av. Professor Egas Moniz

department: Instituto de Medicina Molecular

country: Portugal

institute: Faculdade de Medicina, Universidade de Lisboa

overall_design: To address the role of miRNAs in the differentiation of pro-inflammatory γδ T cell subsets, we compared the ex vivo miRNA expression profile of highly purified CD27+ (γδ27+) and CD27- CCR6+ ( γδ27-) γδ T cells isolated from pooled lymph nodes and spleen of naïve C57BL/6J mice.

first: Nina

last: Schmolka

first: Pedro

middle: H

last: Papotto

first: Paula

middle: V

last: Romero

first: Tiago

last: Amado

middle: J

first: Ana

last: Amorim

last: Rodrigues

first: Katrina

last: Gordon

first: Mark

last: Boldin

first: Karine

last: Serre

first: Amy

last: Buck

first: Anita

middle: Q

last: Gomes

first: Bruno

last: Silva-Santos


title: Implications of CpG islands on chromosomal architectures and modes of global gene regulation

city: Austin

first: Jonghwan

last: Kim

state: TX

address: 2506 Speedway NMS 4.246

department: Department of Molecular Cell and Developmental Biology, Institute for Cellular and Molecular Biology

institute: University of Texas at Austin

type: Genome binding/occupancy profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

summary:
In this study, we present the critical implication of CpG islands (CGI) on the general rules for chromatin structural architectures and gene regulation mechanisms. Through integrative biological big data analyses, we found that the linear gene arrangements in chromosomes harbor the critical evidences for spatial gene segregation and different modes of gene localization between CGI-containing (CGI+) and CGI-less (CGI-) genes within the nucleus. CGI- genes, which are generally located within the nuclear periphery (chromosomal territories) as heterochromatin, are converted to euchromatin and internalized into the nuclear center only when activated. However, CGI-centered regulations keep CGI+ genes from heterochromatin formation and located within nuclear center regardless of their activities. We also show these different localization behaviors make CGI+ and CGI- genes to be regulated by distinct transcriptional regulation mechanisms: CGI- genes are regulated by local bindings of transcription factors, while CGI+ genes are strongly engaged in the 3-dimensional long-range chromosomal interactions.

This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Homo sapiens
Mus musculus

overall_design:
Re-analyses diverse published datasets of ChIP-seq, RNA-seq, gene expression microarray, DNaseI-seq, DamID-seq, MeDIP-seq, ChIA-pet, and Hi-C.

Refer to individual Series


title: The Peroxisome Proliferator-Activated Receptor α is dispensable for cold-induced adipose tissue browning in mice

status: Public on Feb 10 2018

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: Chronic cold exposure causes white adipose tissue (WAT) to adopt features of brown adipose tissue, a process known as browning. Previous studies have hinted at a possible role for the transcription factor Peroxisome Proliferator-Activated Receptor alpha (PPARα) in cold-induced browning. Here we aimed to investigate the importance of PPARα in driving transcriptional changes during cold-induced browning in mice. Male wildtype and PPARα−/− mice were housed at thermoneutrality (28 °C) or cold (5 °C) for 10 days. Whole genome expression analysis was performed on inguinal WAT. In addition, other analyses were carried out. Whole genome expression data of livers of wildtype and PPARα−/− mice fasted for 24 h served as positive control for PPARα-dependent gene regulation.Cold exposure increased food intake and decreased weight of BAT and WAT to a similar extent in wildtype and PPARα−/− mice. Except for plasma non-esterified fatty acids, none of the cold-induced changes in plasma metabolites were dependent on PPARα genotype. Histological analysis of inguinal WAT showed clear browning upon cold exposure but did not reveal any morphological differences between wildtype and PPARα−/− mice. Transcriptomics analysis of inguinal WAT showed a marked effect of cold on overall gene expression, as revealed by principle component analysis and hierarchical clustering. However, wildtype and PPARα−/− mice clustered together, even after cold exposure, indicating a similar overall gene expression profile in the two genotypes. Pathway analysis revealed that cold upregulated pathways involved in energy usage, oxidative phosphorylation, and fatty acid β-oxidation to a similar extent in wildtype and PPARα−/− mice. Furthermore, cold-mediated induction of genes related to thermogenesis such as Ucp1, Elovl3, Cox7a1, Cox8, and Cidea, as well as many PPAR target genes, was similar in wildtype and PPARα−/− mice. Finally, pharmacological PPARα activation had a minimal effect on expression of cold-induced genes in murine WAT.Cold-induced changes in gene expression in inguinal WAT are unaltered in mice lacking PPARα, indicating that PPARα is dispensable for cold-induced browning.

overall_design: Wild type and PPARα-null mice were housed at thermoneutrality (28 °C) or cold (5 °C) for 10 days whereafter inguinal white adipose tissue was subjected to gene expression profiling.

first: Merel

last: Defour

first: Wieneke

last: Dijk

first: Philip

last: Ruppert

first: Emmani

last: Nascimento

first: Patrick

last: Schrauwen

first: Sander

last: Kersten


title: Altered response of macrophages to an inflammatory stimulus in an allergic environment

status: Public on Feb 12 2018

city: Sydney

first: Cristan

last: Herbert

state: NSW

address: High Street

department: School of Medical Sciences/Pathology

country: Australia

institute: University of New South Wales

summary: To investigate how an allergic cytokine environment (associated with increased levels of IL4 and IL-13) alters the response of macrophages to a pro-inflammatory stimulus.

overall_design: Murine macrophage-like cells (RAW264) were grown for 48 hr in the presence or absence of the Th2 cytokines, interleukin-4 and interleukin-13. Groups of cells were then stimulated with recombinant murine IL-33. Total RNA was collected after 4 hours and microRNA expression was assessed using Agilent arrays. Samples from four independent experiments were assessed.

first: Noel

last: Chia

first: Rakesh

middle: K

last: Kumar

first: Paul

last: Foster


title: Identification of genes regulating TRAIL-induced apoptosis in rheumatoid arthritis fibroblasts-like synoviocytes (RA FLS)

city: Montpellier

first: Rachel

last: AUDO

address: 1919 route de Mende

summary: Rheumatoid arthritis (RA) is a chronic systemic inflammatory disease involving primarily the synovial membranes and articular structures of multiple joints. A hallmark of RA is the pseudo-tumoral expansion of fibroblast-like synoviocytes (FLS), as these cells invade and finally destroy the joint structure. RA FLS have been therefore proposed as a therapeutic target.  > TNF-related apoptosis-inducing ligand (TRAIL) has been described as a pro-apoptotic factor on malignant cells. The fact that fibroblasts-like-synoviocytes (FLS) in rheumatoid arthritis RA patients exhibit tumor like features led us to investigate the effect of TRAIL on ex-vivo RA FLS. We have previously described that TRAIL induces apoptosis only in a subset of RA FLS, but an induction of proliferation in the surviving cells. This observation corresponds to the pleiotropic effects of TRAIL observed on primary human tumor cells. We also observed that sensitivity to TRAIL-induced apoptosis varied in  RA FLS  from one patient to another, and was correlated with disease severity. We therefore screened for genes that were differentially expressed in RA FLS sensitive and resistant to TRAIL induced apoptosis in order to understand molecular factors making cells resistant or sensitive to TRAIL induced apoptosis.

overall_design: The sensitivity of synovial fibroblasts from rheumatoid arthritis patients was defined on the percentage of apoptotic cells following TRAIL stimulation: 0-10% corresponded to resistant cells and above 25% to sensitive RAFLS. We performed transcriptomic comparison between twelve sensitive (n=6) and resistant (n=6) synovial fibroblasts. A loop design and dye swap were used for the comparison of resistant and sensitive RAFLS.

last: Audo

first: Michael

last: Hahne

first: Jacques

last: Morel

first: Laurent

last: Journot

first: Dany

last: Severac

first: Christelle

last: Dantec


title: Profiling γ-irradiated invasive Plasmodium falciparum merozoites using a systems biology approach

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

summary: Plasmodium falciparum malaria severely impacts human health. In order to broaden our understanding of merozoite invasion of erythrocytes which is responsible for clinical disease, a P. falciparum γ-irradiated "long-lived merozoite" (LLM) line was investigated. Cell-sieve purified LLM invaded human erythrocytes with an improved efficiency of 10- to 300-fold greater than wild-type (WT) parasites. A comparison of their genomes identified limited changes in the open reading frame of LLM; while only marginal differences were observed in the transcriptomes. Analysis of their proteomes by quantitative mass-spectrometry identified 446 out of 981 proteins of known or unknown function with a significant change in protein abundance (ANOVA p < 0.05). Furthermore, the relative molar concentration of nearly 1100 merozoite proteins was established. Unfortunately, a specific change being responsible for the LLM phenotype was not identified. However, immunoblot analyses of LLM lysates showed proteolytic processing of some proteins of the MSP1 complex and AMA1 were delayed, suggesting that this delayed proteolysis positively impacted merozoite viability and subsequent invasion.

platform_organism:
Plasmodium falciparum
Anopheles gambiae

overall_design: Wild type vs. long-lived merozoite (LLM) Plasmodium falciparum.

first: Krishan

first: Prakash

last: Srinivasan

last: Nold

first: Kathleen

last: Moch

first: Karine

last: Reiter

first: Daniel

middle: E

first: R

middle: B

last: Squires

first: Raul

last: Herrera

first: Vijayaraj

last: Nagarajan

first: Julian

middle: C

last: Rayner

first: Steve

last: Porcella

first: Scott

last: Geromanos

first: J

middle: D

last: Haynes

first: David

middle: L

last: Narum


title: Kinetic of gene expression signatures on ischemia porcine kidney

city: Poitiers

first: Sebastien

last: Giraud

address: CHU de Poitiers, 2 rue de la miletrie

institute: Inserm U1313 IRMETIST, Université de Poitiers, CHU de Poitiers-Service Biochimie

summary: Using an oligonucleotide microarray we performed differential transcriptomic analysis of porcine kidneys subjected to intense ischemic stress which could be observed in donors deceased after circulatory death situation (60 min warm ischemia then 0h, 6h or 24h of cold storage in University of Wisconsin solution) compared to healthy kidneys (n=5 per group). Microarray analysis identified genes which were differentially expressed in different ischemic times versus healthy kidneys (adjusted p value <0.05 + log2 fold change >0.5 or <-0.5).

overall_design: CONTROL samples: 5 independent porcine kidneys (from Large White pig) were removed and then immediately sampled and frozen. WARM ISCHEMIA samples: 5 independent porcine kidneys (from Large White pig) were clamped, removed and maintained clamped 60 min at 37°C, and then immediately sampled and frozen. WARM ISCHEMIA + 6h and 24h COLD STORAGE samples: 5 independent porcine kidneys (from Large White pig) were clamped, removed and maintained clamped 60 min at 37°C, and then flushed with cold (4°C) University of Wisconsin preservation solution (UW) and stored at 4°C, at 6h of cold storage kidneys were sampled and frozen and at 24h of cold storage these same kidneys were sampled and frozen.

first: Delphine

last: Labourdette

first: Lidwine

last: Trouilh

first: Thierry

last: Hauet


title: Asparagine availability governs metastasis in a model of breast cancer

status: Public on Feb 08 2018

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary: Single - cell profiling of patient tumours and of mouse models is revealing that many cancers are constituted of communities of genetically and phenotypically distinct clonal lineages 1 - 12. A functional model of breast cancer heterogeneity revealed that clonal sub - populations proficient at generating circulating tumour cells were not equally capable of forming metastases at secondary sites 13. A combination of differential expression and focused in vitro and in vivo RNAi screens revealed candidate drivers of metastasis discriminating these clones, which were then evaluated in gene expression datasets from breast cancer patients. Among these, Asparagine Synthetase (Asns) expression in a patient's primary tumour was most strongly correlated with later metastatic relapse. Silencing of Asns reduced both metastatic potential in vivo and invasive potential in vitro. Conversely, increasing the availability of extracellular asparagine increased the invasive potential of mouse and human breast cancer cells, and enforced Asns expression promoted metastasis. Decreasing asparagine availability in mice by treatment with L-asparaginase or even by dietary restriction strongly reduced metastasis from orthotopic tumours. Asparagine availability varies betwe en tissues, potentially explaining selective effects on particular steps of tumor progression. Asparagine limitation reduced the production of proteins that promote the epithelial to mesenchymal transition, providing one potential mechanism for how the availability of a single amino acid could regulate metastatic progression.

overall_design: Microarrays were used to analyze primary breast tumors and distant metastases in order to identify biological features associated with distant metastases.

first: Simon

middle: R

last: Knott

first: Elvin

last: Wagenblast

first: Showkhin

last: Khan

first: Sun

middle: Y

last: Kim

first: Mar

last: Soto

first: Michael

last: Wagner

first: Marc

middle: O

last: Turgeon

first: Lisa

last: Fish

first: Nicolas

last: Erard

first: Annika

last: Gable

first: Ashley

last: Maceli

first: Steffen

last: Dickopf

middle: A

last: Cary

first: John

last: Wilkinson

last: Harrell

middle: M

first: Hani

last: Goodarzi

first: George

last: Poulogiannis

first: Gregory

last: Hannon


title: Murine epiSC control vs murine epiSC differentiated into dopaminergic neurons [miRNA]

status: Public on Feb 07 2018

city: Naples

first: Valerio

last: Costa

state: Italy

address: Via P. Castellino, 111

department: Institute of Genetics and Biophysics

country: Italy

institute: National Research Council

summary: Small-RNA profiling of mouse embryonic, epiblast-derived, stem cells (epiSC). epiSC differentiated towards the dopaminergic phenotype were compared to control untreated epiSC. EpiSc were derived from a Pitx3-GFP mouse allowing visualization of dopaminergic (GFP+) differentiation efficiency.

overall_design: EpiSC derived from Pitx3-GFP mice were differentiated for fourteen days. Dopaminergic diffferentiation starts at day 5 with the addition of morphogens SHH and FGF8. Control cells were growth in absence of morphogens. Samples were collected in triplicate at day 5 (before the addition of SHH/FGF) and at day 9 and day 14 for both control and treated cells.

first: Gian

last: Bellenchi

first: Meng

last: Li

first: Dario

last: Greco


title: KRAS induces lung tumorigenesis through microRNAs modulation

city: Manchester

first: Michela

last: Garofalo

address: Wilmslow Road

country: United Kingdom

institute: University of Manchester

summary: We analyzed microRNAs modulated by KRAS wild type or KRAS mutant (G12D).

overall_design: H1299 cells were transfected with an empty vector or a KRAS wild type or a KRAS mutant (G12D) plasmid. Total RNA was extracted and the microRNA expression profile analysed by NanoString.


title: Ribotagging on NSM neurons in C. elegans

status: Public on Feb 09 2018

city: Cambridge

first: Steven

middle: Willem

last: Flavell

state: MA

address: 77 Massachusetts Ave, 46-4243

department: Brain and Cognitive Sciences

institute: MIT

summary: mRNA-seq of adult C.elegans whole-animal and NSM Ribotag samples to identify NSM-enriched genes

overall_design: There are thee independent biological replicate, each containing a whole-animal mRNA-seq dataset and an NSM ribotag mRNA-seq dataset

middle: W

first: Jeffrey

last: Rhoades


title: Murine epiSC control vs murine epiSC differentiated into dopaminergic neurons

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


title: CpG island mediated linear and spatial gene partitioning (other data sets)

first: Jonghwan

last: Kim

summary: In order to elucidate the general rules for gene localization and regulation mediated by CpG islands, we reanalyzed diverse published data of DNaseI-seq, MeDIP-seq, LMNB1-DamID-seq, PolII ChIA-pet, and Hi-C analysis.

first: Samuel

last: Beck


title: Relationship between tolerance and persistence mechanisms in Acinetobacter baumannii strains with AbkAB Toxin-Antitoxin system

city: A Coruña

first: Maria

last: Tomas-Carmona

address: As Xubias, 84

department: Microbiology Department

country: Spain

institute: Instituto de Investigación Biomédica de A Coruña (INIBIC) / Complexo Hospitalario Universitario de A Coruña (CHUAC)

summary: Unknown are the mechanisms of tolerance and persistence associated to several compounds in A.baumannii clinical isolates. Using transcriptomical and microbiological studies, we found a link between bacterial tolerance mechanisms to clorhexidine as well as the development of persistence in presence of imipenem in an A.baumannii strain belonging to ST-2 clinical clone (carbapenem-resistant with OXA-24 ß-lactamase and AbkAB TA system by plasmid). Interestingly, in A.baumannii ATCC17978 strain (carbapenem-susceptible isolate which carries AbkAB TA system by plasmid) showed persistence in presence of imipenem.

overall_design: Medium of four replicates (4 samples and 4 controls) from RNA of the Ab-2_clon_2010 strain (belonging ST-2 clone) x 1 condition (exposure to CHLX). Statistical analysis by DESeq2 and EdgeR

first: Laura

last: Fernández-García

first: Felipe

last: Fernandez-Cuenca

first: María

last: Tomás

first: Lucía

last: Blasco

first: Rafael

last: López-Rojas

last: López

first: Germán

last: Bou

first: Álvaro

last: Pascual


title: Comparison between WT and bes1 in an in vitro tissue culture system, VISUAL

city: Bunkyo-ku

first: Masato

last: Saito

department: Graduate School of Science, Department of Biological Sciences

institute: The University of Tokyo

summary:
We have previously established an in vitro tissue culture system (named VISUAL; Kondo et al., 2016), in which xylem and phloem differentiation can be induced with Arabidopsis thaliana cotyledons
To compare gene expression profiles between WT and bes1 during vascular development, we performed GeneChip analysis using VISUAL.

overall_design: Arabidopsis cotyledons were sampled at 0 h and 72 h after VISUAL induction.

first: Yukiko

last: Sugisawa


title: aCGH of chromosome X in a female patient with ALL and Leri-Weill syndrome

city: Olomouc

first: Petr

last: Vojta

address: Hnevotinska 5

department: Laboratory of experimental medicine

country: Czech Republic

institute: Palacky University

type: Genome variation profiling by genome tiling array

summary: Array CGH of gDNA extracted from leukemic cells at diagnosis of ALL. Goal was to determine CNV polymorphisms linked with phenotype of ALL and Leri-Weill syndrome.

overall_design: ALL cells vs. reference genome control gDNA sample. Biological replicates: 1.

first: H

last: Urbankova

first: M

last: Jarosova


title: Dal81 regulates expression of arginine biosynthesis genes in Candida parapsilosis

city: Dublin

first: Geraldine

last: Butler

address: Belfield, Dublin 4

department: School of Biomolecular and Biomedical Science

country: Ireland

institute: UCD Conway Institute

summary:
Transcriptional profiling of Candida parapsilosis in media with a preferred nitrogen source (ammonium sulfate) and a non-preferred source (isoleucine) to identify genes that are subject to Nitrogen Catabolite Expression.
Gene expression of wild type and dal81 deletion strains were compared during growth in complex nitrogen sources (YPD), in minimal media with a preferred nitrogen source (YNB+ammonium sulfate) and minimal medium with a non-preferred source (GABA).

overall_design: 8 independent samples with three replicates of each, generating 24 samples.

first: Mihaela

last: Ola

first: Siobhan

last: Turner


title: Murine epiSC control vs murine epiSC differentiated into dopaminergic neurons [mRNA]

first: Valerio

last: Costa

summary: Transcriptional profiling of mouse embryonic, epiblast-derived, stem cells (epiSC). epiSC differentiated towards the dopaminergic phenotype were compared to control untreated epiSC. EpiSc were derived from a Pitx3-GFP mouse allowing visualization of dopaminergic (GFP+) differentiation efficiency.

first: Gian

last: Bellenchi

first: Meng

last: Li

first: Dario

last: Greco


title: Roles of the Brca2 and Wapl complexes with Pds5 in sister chromatid cohesion, cohesin localization, and gene expression [ChIP-seq]

status: Public on Feb 05 2018

city: Saint Louis

first: Dale

last: Dorsett

state: MO

address: 1100 South Grand Boulevard

department: Biochemistry and Molecular Biology

institute: Saint Louis University School of Medicine

summary: The Pds5, Wapl and Brca2 proteins were mapped by ChIP-seq, and the effects of their depletion on the binding of cohesin subunits and the Nipped-B cohesin loader were examined by ChIP-seq

overall_design:
Comparison of sister chromatid cohesion protein binding in control ML=DmBG3-c2 cells and cells depleted for proteins regulating sister chromatid cohesion proteins

This series includes input samples re-used from GSE83959 and GSE100548


title: CpG island mediated linear and spatial gene partitioning (RNA-seq)

first: Jonghwan

last: Kim

summary: We reanalyzed published RNA-seq data to study 1) the genomic landscapes near surrounding regions of transcriptional start sites with regard to the gene expression activities and 2) the gene expression change upon transcription factor (MYBL1, ATF4) depletion. Raw data were downloaded from Sequence Read Archive (SRA) in National Center for Biotechnology Information (NCBI) database. FASTQ files were extracted with the SRA Toolkit version 2.5.5 and aligned using STAR 2.4.2 onto the mouse and human genome (mm9 and hg19, respectively). Gene expression was calculated as RPKM values using rpkmforgenes.py (Ramsköld et al., 2009).

overall_design: RNA-seq gene expression analyses in diverse mouse and human samples.

first: Samuel

last: Beck


title: A vaginal tract signal detected by the GBS SaeRS system elicits transcriptomic changes and enhances murine colonization.

status: Public on Feb 06 2018

city: Chicago

first: Laura

last: Cook

state: IL

address: 900 S. Ashland Avenue (870)

department: College of Pharmacy

institute: University of Illinois at Chicago

summary: Streptococcus agalactiae (Group B Streptococcus, GBS) can colonize the human vaginal tract leading to both superficial and serious infections in adults and neonates. To study bacterial colonization of the reproductive tract in a mammalian system, we employed a murine vaginal carriage model. Using RNASeq, the transcriptome of GBS growing in vivo during vaginal carriage was determined. Over one-quarter of the genes in GBS were found to be differentially regulated during in vivo colonization as compared to laboratory cultures. A two-component system (TCS) homologous to the staphylococcal virulence regulator SaeRS was identified as being up-regulated in vivo. One of the SaeRS targets, pbsP, a proposed GBS vaccine candidate, was shown to be important for colonization of the vaginal tract. A component of vaginal lavage fluid acted as a signal to turn on pbsP expression via SaeRS. These data demonstrate the ability to quantify RNA expression directly from the murine vaginal tract and identify novel genes involved in vaginal colonization by GBS. They also provide more information about the regulation of an important virulence and colonization factor of GBS, pbsP, by the TCS SaeRS.

overall_design: RNASeq data from WT and mutant GBS samples taken from liquid culture or the murine vaginal tract

first: Michael

last: Federle

first: Hong

last: Hu

first: Mark

last: Maienschein-Cline


title: CpG island mediated linear and spatial gene partitioning (MOE430V2)

type:
Expression profiling by array
Third-party reanalysis

summary: In order to study the gene expression change upon transcription factor (MYOD1, SPI1) induction, we reanalyzed published gene expression microarray data. Raw data were preprocessed and normalized with the Robust Multi-array Average (RMA)(Irizarry et al., 2003) method.

overall_design: Microarray gene expression profile upon MYOD1 induction in mouse embryonic fibroblast cells and SPI1 recovery in myeloid progenitors.


title: PARP14 controls the nuclear accumulation of a subset of type I Interferon-inducible proteins [reanalysis]

city: Milano

first: Viviana

last: Piccolo

state: Milano

address: Via Adamello 16

department: Department of Experimental Oncology

institute: European Institute of Oncology (IEO)

summary: The enzymes of the poly-ADP-ribose polymerase (PARP) super-family control many relevant cellular processes, but a precise understanding of their activities in different physiological or disease contexts is largely incomplete. We found that transcription of several PARP genes was dynamically regulated upon macrophage activation by several inflammatory stimuli. Specifically, PARP14 was strongly induced by endotoxin stimulation and translocated to the nucleus in stimulated cells. Quantitative mass spectrometry analysis showed that PARP14 bound to a group of interferon-stimulated gene (ISG)-encoded proteins, most with an unknown function, and it was required for their nuclear accumulation. Moreover, PARP14 depletion attenuated transcription of primary antiviral response genes regulated by the transcription factor IRF3, including Ifnb1, thus reducing IFNβ production and activation of ISGs involved in the secondary antiviral response. Overall, these data hint at a role of PARP14 in the control of antimicrobial responses and specifically in nuclear activities of a subgroup of ISG-encoded proteins.

overall_design: Nascent RNA sequencing of primary bone marrow-derived macrophages (BMDM)

first: Greta

last: Caprara

first: Elena

last: Prosperini

first: Gianluca

last: Sigismondo

first: Alessia

last: Melacarne

first: Alessandro

last: Cuomo

last: Boothby

first: Maria

last: Rescigno

first: Tiziana

last: Bonaldi

first: Gioacchino

last: Natoli


title: Replication origin mapping of Cdc13-Cdc2 cells in different G1 extension

status: Public on Feb 04 2018

city: Bordeaux

first: Pei-Yun Jenny

last: Wu

address: 1 Rue Camille Saint Saens

institute: Institute of Biochemistry and Cellular Genetics

summary:
Identification of sites of replication initiation by copy number analysis, comparing samples before and after entry into S phase.
Experiments were performed in Cdc13-Cdc2 strain in which G1 phase has been delayed by 5 or 15 minutes.

overall_design: Comparison of samples before and after S phase entry; dye-swap experiments were performed and averaged.

first: Anthony

last: Perrot

first: Pei-Yun


title: Replication origin mapping of Cdc13-Cdc2 G1 block release in different CDK activity levels

summary:
Identification of sites of replication initiation by copy number analysis, comparing samples before and after entry into S phase.
Experiments were performed in Cdc13-Cdc2 strain after G1 block for 165 min and release in 1, 2.5, 4 or 6µM inhibitor.


title: ChIP-on-chip of Cdc45 in S. pombe

summary: ChIP-on-chip of Cdc45 in synchronized cells operating with the analog-sensitive CDK fusion protein (Cdc13-Cdc2). Cells were released from a G2 block or from a G2 block followed by an extended G1 (G1+ 15 min extension). For the G2 block, samples were collected 30 minutes after release. For the G1+15 extension, samples were collected 3 minutes after release. Timepoint of collection was based on qPCR experiments showing Cdc45 binding at origins of replication.

overall_design: Each IP was compared to its reciprocially labeled input sample. Duplicates for every condition

first: Blanca

last: Gómez-Escoda


title: Comparison of primary vs immortalized murine hepatocytes

status: Public on Feb 03 2018

city: Hannover

first: Oliver

last: Dittrich-Breiholz

address: Carl-Neuberg-Str. 1

department: Research Core Unit Genomics

country: Germany

institute: Medical School Hannover

summary:
Fundamental research and drug development for personalized medicine necessitates cell cultures from defined genetic backgrounds. However, providing sufficient numbers of authentic cells from individuals poses a challenge. Here, we present a new strategy for rapid cell expansion that overcomes current limitations. Using a small gene library, we expanded primary cells from different tissues, donors and species. Cell type specific regimens that allow the reproducible creation of cell lines were identified. In depth characterization of a series of endothelial and hepatocytic cell lines confirmed phenotypic stability and functionality. Applying this technology enables rapid, efficient and reliable production of unlimited numbers of personalized cells. As such, these cell systems support mechanistic studies, epidemiological research and tailored drug development.
In these experiments primary murine hepatocytes were compared to immortalized murine hepatocytes with respect to their global gene expression pattern.

overall_design: The global gene expression profile of primary and immortalized hepatocytes (cell line e-mHepA) was analyzed. In addition the murine hepatocyte cell line Hepa1-6 and murine fibroblasts were included as controls (two samples each). The immortalized murine hepatocytes were cultivated on normal tissue cultures plastic (2D samples) and as spheroids (3D samples). The hepatocyte cell line e-mHepA was immortalized by the genes TAg, KLF4, ID3 and Core. Each sample was run in duplicate.

first: Christoph

last: Lipps

first: Tom

last: Wahlicht

first: Tobias

last: May

first: Dagmar

last: Wirth


title: miRNA profiling of Macaca mulatta colonic epithelium samples from chronic SIV infected rhesus macaques

status: Public on Feb 01 2018

city: San Antonio

first: Mahesh

last: Mohan

state: Texas

address: 8715 West Military Road

department: Host Pathogen Interaction Program

institute: Southwest National Primate Research Center

summary: The study describes miRNA expression in colonic epithelium of chronic SIV-infected rhesus macaques. We profiled and characterized miRNA/mRNA expression exclusively in colonic epithelium (CE) of 12 chronically SIV-infected and 8 control rhesus macaques (RMs). About 46 miRNAs were differentially expressed (DE) (20-up and 26-down) in CE during chronic SIV infection. Using TargetScan, we bioinformatically crossed the predicted targets of DE miRNAs to genome-wide transcriptomic data and identified several critical miRNA-mRNA pairings that suggested miRNA-mediated regulation of aberrant epithelial gene expression in CE. Immunofluorescence, luciferase reporter and miRNA overexpression studies confirmed the ability of miR-130a and miR-212 to bind the 3’ UTR and downregulate protein expression of occludin (OCLN) and peroxisome proliferator activator receptor gamma (PPAR), respectively, two proteins with pivotal roles in epithelial barrier function. MiR-130a and miR-212 overexpression in Caco-2 cells significantly reduced transepithelial electrical resistance (TEER). Interestingly, delta-9-tetrahydrocannabinol (9-THC) treatment restored TEER to levels observed with control miRNA mimic. Finally, ex-vivo 9-THC treatment of colon tissue from chronically SIV-infected RMs significantly increased PPAR gene expression. Our findings suggest that dysregulated miR-130a and miR-212 expression in CE during chronic HIV/SIV infection can facilitate epithelial barrier disruption by downregulating OCLN and PPAR protein expression. Most importantly, our results highlight the beneficial effects of cannabinoids on epithelial barrier function in not just HIV/SIV but potentially other chronic intestinal inflammatory diseases.

overall_design: Colonic epithelium samples were isolated from 12 chronically SIV-infected and 8 uninfected control rhesus macaques.

first: M


title: Epigenetic dysregulation of the Drp1 binding partners MiD49 and MiD51 increases mitotic mitochondrial fission and promotes pulmonary arterial hypertension: mechanism and therapeutic implications

status: Public on Jan 31 2018

city: Kingston

first: Stephen

last: Archer

state: Ontario

address: 94 Stuart Street

department: Medicine

institute: Queen's University

summary:
Mitotic fission is increased in hyperproliferative, apoptosis-resistant diseases, such as pulmonary arterial hypertension (PAH). PAH’s fissogenic phenotype includes activation of the fission mediator, dynamin related protein 1 (Drp1), which must complex with its adaptor proteins to cause fission. Drp1-induced fission has been therapeutically targeted in experimental PAH. Here we examine the role of two recently discovered, poorly understood, Drp1 adapter proteins, mitochondrial dynamics protein of 49 and 51 kDa (MiD49 and MiD51) in normal vascular cells and explore the role of their dysregulation in the pathogenesis of PAH. MiDs are increased in PAH PASMC. This accelerates Drp1-mediated mitotic fission, which increases cell proliferation and decreases apoptosis. Silencing MiDs (but not Fis1 or MFF) promotes mitochondrial fusion and G1-phase cell cycle arrest through an ERK1/2 and CDK4-dependent mechanism. Augmenting MiDs in normal cells causes fission and recapitulates the PAH phenotype. MiD upregulation results from decreased microRNA-34a-3p (miR-34a-3p) expression. Circulatory miR34a-3p expression is decreased in PAH patients as well as in preclinical models of PAH. Silencing MiDs or augmenting miR-34a-3p regresses experimental PAH.
We used microarrays to identify differences in miR expression in pulmonary artery smooth muscle cells (PASMC) taken from either pulmonary arterial hypertension patients or healthy controls

overall_design: PASMCs from PAH (n=6) or healthy controls (n=3) were compared.

first: Kuang-Hueih

last: Chen

first: Asish

last: Dasgupta

first: Jianhui

last: Lin

first: Francois

last: Potus

first: Sebastien

last: Bonnet

first: James

last: Iremonger

first: Jennifer

last: Fu

first: Jeffrey

last: Mewburn

first: Danchen

first: Kimberly

last: Dunham-Snary

first: Anne

last: Theilmann

first: Zhi-Cheng

last: Jing

first: Charles

last: Hindmarch

first: Mark

last: Ormiston

first: Allan

last: Lawrie


title: Gene expression profiles from mouse pancreatic islets at ZT8 or ZT20

city: Lille

first: Lefebvre

last: Philippe

state: Nord

address: Blvd Pr. J.Leclerc

institute: Inserm

summary:
Expression studies in several models of type 2 Diabetes have suggested that exocytosis contributes to the modulation of insulin secretion during the 24h cycle. In agreement with the activity and feeding pattern of nocturnal rodents, we find that C57/Bl6J mice exhibit higher insulin secretion during the dark phase (ZT20 vs ZT8).  Glucose-induced insulin secretion is increased by 21% despite normal intracellular Ca2+ signaling and depolarization-evoked exocytosis as measured by whole-cell capacitance measurements. This paradox is explained by a 1.37-fold increase in beta cell insulin content. Ultramorphological analysis show that vesicle size and density are unaltered but the intravesicular content per granule is modulated during the circadian rhythm. Proinsulin levels were not statistically different between the two time points despite a trend for reduction at ZT20. Islet glucagon content was inversely proportional to insulin content. Microarray data identified the differential expression of 301 transcripts of which, 54 known genes and 26 miRNA, including clock genes such as Bmal1 and Rev-erb . Differential expression of C2cd4b may contribute to the modulation of insulin content.  Mice -cell secretion during the 24h cycle may rely on several distinct cellular functions but late night increase in insulin secretion depends solely on granule insulin content.
A total of 301 genes were differentially expressed between ZT8 vs ZT20 islets . A majority were upregulated (199 between 1.3 to 2.71 fold) whilst 102 were down-regulated (<-1.3 fold). Given the focus of our study, current literature and our own results, genes involved in exocytosis, insulin production and of course, circadian rhythms were particularly interesting.

overall_design: 10 samples were genrated and splitted in 2 groups: ZT8 and ZT20.

first: S

last: Collins

first: P

last: Lefebvre


title: Gene expression profile in response to NGG1 deletion during filament formation in Spider medium

city: Beijing

first: Dedong

last: Li

state: Beijing

address: Fuxing Road 28

department: department of clinical pharmacology

institute: PLA General Hospital

summary: Transcriptional profiling of Candida albicans comparing NGG1 deletion mutant cells with the wild-type cells in Spider medium

overall_design: The NGG1 deletion mutant ngg1Δ/Δ and the wild-type strain SC5314 were used to perform the microarray experiments. Condition: ngg1Δ/Δ vs SC5314 in Spider midium. Biological replicates: 3 NGG1 deletion mutant ngg1Δ/Δ samples (test group), 3 wild-type strain SC5314 samples (control group), independently grown and harvested.


title: Divergent N-deficiency-dependent senescence initiation and transcriptome response in developmentally old and young Brassica napus leaves

city: Berlin

first: Reinhard

last: Kunze

state: Berlin

address: Albrecht-Thaer-Weg 6

department: Institute of Biology

institute: Freie Universität Berlin

summary: To identify oilseed rape genes with a potential role in N-remobilization during leaf senescence of developmentally old leaves in the lower canopy and young leaves in the upper canopy, transcriptomes of leaf number 4 and leaf number 8 of B. napus (cultivar Mozart) were analysed at different harvest time points under mild N deficiency and optimal N fertilization.

overall_design: Brassica napus, spring cultivar Mozart, was grown in seasonal climate simulating growth chambers under mild N defciency (NL: 75 kg N/ha NH4NO3) or optimal N supply (NO: 150 kg N/ha NH4NO3). The transcriptomes of leaf number 4 at  78, 85, 92 and 99 days after sowing (DAS) and leaf number 8 at 92 and 106 DAS were determined in three separate plants each (biological replicates R1 - R3).

first: Vajiheh

middle: S

last: Rizi


title: Allergic Airway Disease is Dependent on Methylene-Tetrahydrofolate Reductase (expression)

city: Aurora

first: Kenneth

last: Eyring

state: CO

address: 12700 East 19th Avernue, 8611

department: Department of Medicine

institute: University of Colorado School of Medicine

summary:
RATIONALE: The development and progression of asthma are strongly influenced by environmental exposures.  We have demonstrated that mice exposed to a diet enriched with methyl donors during vulnerable periods of fetal development can enhance the heritable risk of allergic airway disease through epigenetic changes.
OBJECTIVES: Since there is conflicting evidence on the role of folate in modifying allergic airway disease risk, we hypothesized that blocking folate metabolism through the loss of methylene-tetrahydrofolate reductase (MTHFR) activity would reduce the allergic airway disease phenotype.
METHODS: Using a house dust mite (HDM) induced model of allergic airway disease, we tested the effect of MTHFR on disease severity.
MEASUREMENTS AND MAIN RESULTS: Loss of MTHFR alters single carbon metabolite levels in the lung and serum including elevated homocysteine and cystathionine and reduced methionine.  HDM-treated C57BL/6MTHFR-/- mice demonstrate significantly less airway hyerreactivity (AHR) compared to HDM-treated C57BL/6 mice.  Furthermore, HDM-treated C57BL/6MTHFR-/- mice compared to HDM-treated C57BL/6 mice have reduced whole lung lavage (WLL) cellularity, eosinophilia, and IL-4/IL-5 cytokine concentrations.  The effect of MTHFR loss on HDM-induced allergic airway disease was reversed by betaine supplementation. 737 genes are differentially expressed and 146 regions are differentially methylated in lung tissue from HDM-treated C57BL/6MTHFR-/- mice and HDM-treated C57BL/6 mice.  Additionally, analysis of methylation/expression relationships identified 503 significant correlations.
CONCLUSION: Collectively, these findings indicate that single carbon metabolism warrants further investigation as a disease modifier in allergic airway disease.

overall_design: Gene expression profiles of lung in MTHFR-/- mice treated with house dust mite (HDM, n = 9) or saline (n = 5) or wild-type (WT) mice treated with house dust mite (HDM, n = 9) or saline (n = 6)

first: Brent

last: Pedersen

middle: N

last: Maclean

first: Sally

middle: P

last: Stabler

first: Ivana

middle: V

last: Yang

first: David

last: Schwartz


title: Osteopontin Deficiency Amerliorates Alport Kindey Pathology

status: Public on Jan 30 2018

city: Miami

first: Lina

last: Shehadeh

state: FL

institute: University of Miami

summary: Kidneys were snap frozen from 2 month old wild type, Col4a3-/-, or Col4a3-/-OPN-/- mice. RNA was isolated using Mirvana Paris kit.

overall_design: Kidneys were snap frozen from 2 month old wild type (n=2), Col4a3-/- (n=3), or Col4a3-/-OPN-/- (n=3) mice. RNA was isolated using Mirvana Paris kit.


title: Ovarian cancer cell line response to Snail depletion

status: Public on Jan 27 2018

city: kyoto

first: Mana

last: Taki

state: kyoto

address: 54, shogoinkawahara-cho, sakyo-ku

department: Gynecology and Obstetrics

institute: Kyoto University

summary:
Analysis of mouse ovarian cancer cell line HM-1 transfected with shRNA targeting Snail, an EMT inducer.
Anti-tumor immuty in state of EMT remains unclear. We focused on Snail, a major EMT inducer, and explored the influence of Snail on immune ivasion into ovarian tumors by generating Snail knockdown cell line. Elucidating the mechanisms of Snail-induced immune evasion will lead to the development of novel treatment strategies for tumor undergoing EMT.

overall_design: HM-1 mouse ovarian cancer cells were transfected with GIPZ Lentivial Mouse Snai1 shRNA sh1, sh2 and non-silencing control.

first: Kaoru

last: Abiko


title: Gene expression analyses from 3-day testes of D. melanogaster

status: Public on Jan 25 2018

city: Iowa City

first: Pamela

last: Geyer

state: Iowa

address: 375 Newton Rd

department: Biochemistry

institute: University of Iowa

summary: Suppressor of Hairy-wing [Su(Hw)] is a globally expressed twelve-zinc finger transcription factor in Drosophila. Su(Hw) is well-known for its role in establishing the gypsy insulator within the gypsy retrotransposon. A direct role of Su(Hw) in gene activation and repression was uncovered through the study in the Drosophila oogenesis, revealing that Su(Hw)-dependent repression of neuronal genes is essential for egg production. Motivated from the spatially restricted expression of Su(Hw) in the testis, we investigated the role of Su(Hw) in spermatogenesis. We discovered that Su(Hw) is required for sperm development and male fertility. Data presented here examined the transcriptional role of Su(Hw) in the Drosophila testis. These studies identified ~400 genes with altered expression in the absence of Su(Hw). Coupled with whole-genome Su(Hw) binding profiles, we identified 145 direct targets of Su(Hw) regulation, of which ~80% show increased transcription upon Su(Hw) loss. Upregulated Su(Hw) targets are enriched for neuronal expression, emphasizing that Su(Hw) represents a functional homolog of mammalian REST that represses neuronal gene expression in non-neuronal tissues.

overall_design: RNAs were isolated from 3-day teses of wild type (Canton S and BL15598) and su(Hw) null mutants (su(Hw)2/v and su(Hw)A2663/2) Drosophila melanogaster.

first: Tingting

last: Duan

middle: K


title: MicroRNA expression in bovine satellite cells at 6th day of in vitro differentiation - myotubes (Hereford & Limousin vs Holstein-Freisian cattle)

city: Warsaw

first: Tomasz

last: Sadkowski

address: Nowoursynowska 159

department: Department of Physiological Sciences

country: Poland

institute: Warsaw University of Life Sciences - SGGW

summary: miRNA profiling of bovine satellite cells (BSC) differentiated into myotubes (6th day of in vitro differentiation). BSC isolated from m. semitendinosus of beef (Hereford & Limousine) and dairy (Holstein-Friesian) cattle. Goal was to determine differences in miRNA expresion during in vitro myogenesis in beef vs dairy cattle used as a control.

overall_design: Three-condition experiment. Hereford (HER) derived BSC (test1) & Limousin (LIM) derived BSC (test2) vs Holstein-Friesian derived BSC (control). Biological replicates: 8 reps of examined condition HER, 8 reps of examined condition LIM, 8 control replicates HF

first: Anna

last: Ciecierska


title: Aging African Green Monkeys manifest transcriptional, pathological, and cognitive hallmarks of human Alzheimer’s disease

city: West Point

first: Keith

last: Tanis

address: 770 Sumnetown Pike

institute: Merck & Co, Inc

summary: While many preclinical models of Alzheimer’s disease (AD) have been reported, none fully recapitulate the disease. In an effort to identify an appropriate preclinical disease model, we characterized age-related changes in two higher order species, the African Green Monkey (AGM) and the rhesus macaque. Gene expression profiles in the dorsolateral prefrontal cortex and the visual cortex showed age-related changes in AGMs that are strikingly reminiscent of AD, whereas aged rhesus were most similar to healthy elderly humans.  Biochemically, age-related changes in AGM cerebrospinal fluid levels of tau, phospho-tau and amyloid beta were consistent with AD.  Histologically, aged AGMs displayed pathological hallmarks of the disease, plaques, and two AGMs showed evidence of neurofibrillary tangle-like structures.  We hypothesized and confirmed that AGMs have age-related cognitive deficits via a prefrontal cortex-dependent cognition test, and that symptomatic treatments which improve cognition in AD patients show efficacy in AGMs. These data suggest that the AGM could represent a novel and improved translational model to assist in the development of therapeutics for AD.

sample_organism:
Chlorocebus aethiops
Macaca mulatta

platform_organism:
Chlorocebus aethiops
Macaca mulatta

overall_design: Examination of Transcriptome in African Green and Rhesus Dorsal Lateral Prefrontal Cortex and Visual Cortex with age

middle: Q

first: Jason

last: Uslaner


title: Expression data from D.melanogaster larvae with a constitutively active Imd in the fat body

status: Public on Jan 24 2018

city: Edmonton

first: Saeideh

last: Davoodi

state: Alberta

address: 116 st and 85 ave

department: Medical Microbiology and Immunology

institute: University of Alberta

summary:
Activation of innate immune responses in the Drosophila larval fat body affects the physiological host responses.
In order to characterize the effect of the activated immune responses in the fat body on the Drosophila, we used whole-genome microarray analysis and found that activation of the immune deficieny pathway (Imd) in the fat body alters the transcriptional profiles of Drosophila larvae. As we expected many of genes involved in regulation of antimicrobial peptides were upregulated in the larvae with elevated Imd activity in the fat body. Notably, we found activatioan of Imd in the fat body negatively affects expression of genes involved in glycolysis, energy production and insulin signaling pathway. Overall, our analysis showed that activation of innate immune signaling in the larval fat body significantly affects cellular pathways that regulate metabolism.

overall_design: Genotype control larvae and larvae with a constitutively active Imd in the fat body were raised on regular food until they reached third instar larvae stage. Whole larvae were used for RNA extraction and RNA was hybridized to Affymetrix GeneChip®Drosophila Genome 2.0 arrays in order to investigate the effects of activation of innate immune responses in the fat body on the transcriptional profile of Drosophila larvae.

first: Edan

last: Foley


title: Transcriptomic analysis of Dinoroseobacter shibae DFL12T in response to phage infection

status: Public on Jan 20 2018

city: Xiamen

first: Yunlan

address: Zhourong quan BLV 2-306, Xiamen University, Xianan, Xiamen

institute: Xiamen university

summary: Dinoroseobacter shibae DFL12T was cultured with/without phage R2C, and gene expression was analyzed at 60 min and 140 min during the incubation

overall_design: Infected and uninfected Dinoroseobacter shibae DFL12T were sampled at two time points and two biological replicates sample for each experiment

first: Rui

last: Zhang


title: Pathways impacted by genomic alterations in pulmonary carcinoid tumors

status: Public on Jan 26 2018

city: Rochester

first: Michael

last: Asiedu

state: MN

address: 200 Fisrt ST SW

department: Surgery

institute: Mayo Foundation for Medical Education and Research

summary: Pulmonary carcinoid tumors account for up to 5% of all lung malignancies in adults, comprise 30% of all carcinoid malignancies, and are defined histologically as typical carcinoid (TC) and atypical carcinoid (AC) tumors. The role of specific genomic alterations in the pathogenesis of pulmonary carcinoid tumors remains poorly understood. We sought to identify genomic alterations and pathways that are deregulated in these tumors to find novel therapeutic targets for pulmonary carcinoid tumors.We performed integrated genomic analysis of carcinoid tumors comprising whole genome and exome sequencing, mRNA expression profiling and SNP genotyping of specimens from normal lung, typical and atypical carcinoid, and small cell lung carcinoma (SCLC) to fully represent the lung neuroendocrine tumor spectrum. Pathway analysis of of CNV and gene expression data suggested deregulation of the NF-ĸB and MAPK/ERK pathways. This study identified mutated genes affecting cancer relevant pathways and biological processes that could provide opportunities for developing targeted therapies for pulmonary carcinoid tumors.

overall_design: RNA for gene expression analysis was extracted using the RNeasy Mini Kit and TissueLyser (Qiagen) according to the manufacturer's instructions. About 100-200 ng of total RNA were used for whole genome mRNA expression profiling which was performed on 64 human lung samples including 31 typical carcinoid, 11 atypical carcinoid, 12 small cell lung cancers and 9 adjacent normal lung tissues using the Illumina Human WG-6_v2 BeadArray Chip in the Mayo Clinic Advanced Microarray Shared Resource. Gene expression data were loaded into the Beadstudio v3 software (Illumina Inc., San Diego, CA) and data were normalized using the cubic spline method. Data were analyzed with Partek Genomics suite software.  The normalized data were subsequently analyzed by principal component analysis (PCA) to determine if any intrinsic clustering or outliers existed within the data set. ANOVA analysis, including Fold Change, p-value and False Discovery Rate (FDR) were performed to compare the following 4 groups 1) Typical carcinoid vs. Atypical carcinoid; 2) Carcinoid vs. Normal tissue; 3) Carcinoid vs. Small cell lung cancer; and 4) Small cell lung cancer vs. Normal tissue. A total of 1181 genes were filtered across all groups using criteria of P<0.001 and |Fold change| >3. There were 683, 416 and 612 genes filtered separately in each of groups 2, 3 and 4.

first: Dennis

last: Wigle


title: Genome-wide maps of c-Myc binding sites in myoblasts and myotubes

status: Public on Jan 17 2018

city: Guangzhou

first: Wen

last: Luo

state: Guangdong

address: Wushan

institute: South China Agricultural University

summary: By applying ChIP-seq, we generated genome-wide maps of c-Myc in skeletal myoblasts and myotubes. We found that c-Myc binds to 19354 confident target with a large portion residing in the intergenic regions. In addition, c-Myc was found to regulate many loci. Further detailed study revealed that c-Myc can regulate some genes, miRNAs, and lincRNAs which are fucntional in skeletal myogenesis. In this study, we identified a c-Myc induced regulatory pathway in myogensis.

overall_design: Examination of c-MYC targets in myoblasts versus myotubes

first: Xiquan


title: An integrated analysis of phosphorus starvation responses in the diatom Pheaodactylum tricornutum

city: Trondheim

first: Per

last: Winge

address: Høgskoleringen 5e

department: Department of Biology

country: Norway

institute: Norwegian University of Science and Technology

summary: 48 h and 72 h after P, transcriptional profiles of P-depleted (-P) and P-replete (+P) cultures depletion were integrated with metabolite and physiological data. It resulted in identification of essential metabolic pathway remodeled under P deficiency. The most significant inductions were related to proteins involved in phosphate acquisition and scavenging, such as phosphate transporters, alkaline phosphatases and nucleotidases. P-depleted cells also showed photosynthesis, nitrogen assimilation, and nucleic acid and ribosome biosynthesis. Repression of the Calvin cycle along with induction of cytosolic glycolysis and the pentose phosphate pathway led to carbon reallocation. Furthermore, we observed changes in the lipid composition of P-depleted cultures through degradation of phospholipids and induction of biosynthetic pathways of non-phosphorus containing lipids.

overall_design: Axenic cultures of Phaeodactylum tricornutum were grown in f/2 medium and kept in exponential growth at 15ºC under continuous white fluorescent light (60 µmol photons m-2 s-1) inside the shaking incubator for three weeks. Three replicates and parallels of the start culture were transferred to media supplemented with complete f/2 nutrients (replete) or f/2 without phosphate (deplete). Cells were incubated in batch cultures with a start cell density of 5×104 ml-1 in 75 cm2 sterile culture flasks and volume of 220 ml. Cell counting and variable in vivo Chl a fluorescence (Fv/Fm) was measured daily. For the other experiments, samples were harvested 48 h and 72 h after the beginning of the treatment.

first: Leila

last: Alipanah

first: Jens

last: Rohloff

first: Javad

last: Najafi

first: Tore

last: Brembu

first: Atle

last: Bones

first: Torfinn

last: Sparstad


title: RNA-sequencing of chicken primary myoblasts and myotubes

summary: Chick is an ideal model system for myogenesis study. Lots of genes would change their expression during myogenesis, however, is there any difference about gene expression between chick and mice? Our study represents the first detailed analysis of the transcriptomes of chicken primary myoblasts and myotubes, with biologic replicates, generated by RNA-seq technology. The data reported here may provide an important understanding of the genes involved in the regulation of chicken myogenesis.

overall_design: Examination of differentially expressed genes in chicken myoblasts versus myotubes


title: CpG island mediated linear and spatial gene partitioning (ChIP-seq)

status: Public on Feb 15 2018

city: Austin

first: Jonghwan

last: Kim

state: TX

address: 2506 Speedway NMS 4.246

department: Department of Molecular Cell and Developmental Biology, Institute for Cellular and Molecular Biology

institute: University of Texas at Austin

summary: In order to elucidate the general rules for gene localization and regulation mediated by CpG islands, we reanalyzed published ChIP-seq data of CXXC domain, H3K9me3, KDM2A, SUV39H1, ATF4, MYBL1, MYOD1, SPI1, and CTCF. Raw data were downloaded from Sequence Read Archive (SRA) in National Center for Biotechnology Information (NCBI) database. FASTQ files were extracted with the SRA Toolkit version 2.5.5 and aligned using Bowtie 2.2.5 onto the mouse and human genome (mm9 and hg19, respectively). For the identification of factor binding sites, model-based analysis for ChIP-seq peak caller (MACS 1.4.2) was used with a p-value cutoff of 1e-5.

overall_design: Analyses of published ChIP-seq data of 7 DNA binding proteins and CXXC domain, H3K9me3 marks  and author provided controls.

first: Samuel

last: Beck


title: Blocking and randomization to improve molecular biomarker discovery

status: Public on Jan 10 2018

city: New York

first: Li-Xuan

last: Qin

state: New York

address: 485 Lexington Ave

department: Epidemiology and Biostatistics

institute: Memorial Sloan Kettering Cancer Center

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

overall_design: Refer to individual Series


title: Endothelial cells modulate the cardiac stress response via two secreted lncRNAs

status: Public on Dec 31 2017

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

summary: We wanted to assess how reduced GATA2 levels in endothelial cells might lead to cardiac failure

overall_design: We isolated endothelial cells from hearts of control or G2-EC-KO mice and analyzed global gene expression by microarray

first: J

last: Heineke

first: N

last: Froese

first: R


title: Expression data from transdetermined Drosophila eye antennal imaginal disc by winged eye overexpression.

city: Sendai

first: Keita

last: Masuko

address: Aoba 6-3, Aramaki, Aoba-ku,

department: Pharmaceutical Science

country: Japan

institute: Tohoku University

summary:
Drosophila imaginal disc cells exhibit a remarkable ability to switch cell fates under various perturbations, a phenomenon known as transdetermination (TD). The winged eye (wge) gene induces eye-to-wing TD by its overexpression in eye imaginal discs using eye specific Gal4 driver (eyeless-Gal4). Gene network controlling this process, however, is largely unclear. Additionally, we identified that heterochromatin-related histone methyltransferase Su(var)3-9 is essential for wge-mediated TD.
We used microarray to detail the global gene network underlying wge-mediated eye-to-wing TD, and the involvement of Su(var)3-9 in the gene network.

overall_design: Third instar larval eye imaginal discs were dissected for RNA extraction and hybridization on Affymetrix microarray. Flies from each genotype were used (I: eyeless-Gal4, II: UAS-wge, III: ey-Gal4; UAS-wge (ey > wge), IV: ey-Gal4 UAS-wge; Su(var)3-91/Su(var)3-92). Three biologic replicates were obtained for each.

first: Shoichiro

last: Kurata


title: MicroRNA-155 is a direct target of Meis1, but not a driver in acute myeloid leukemia

status: Public on Dec 01 2017

city: Gothenburg

first: Lars

last: Palmqvist

address: Sahlgrenska University Hospital

department: Institute of Biomedicine

country: Sweden

institute: University of Gothenburg

summary: OBJECTIVE: The microRNA miR-155 is upregulated by Hoxa9 and Meis1, and accelerate the onset of acute myeloid leukemia (AML) together with Hoxa9 but through largely unknown molecular mechanisms. To further resolve these mechanisms, we performed a gene expression profiling, in the context of Hoxa9 leukemogenesis with our without overexpression of miR-155. RESULTS: Gene expression profiling of a Hoxa9 preleukemic cell line transduced with miR-155 leads to differential expression of multiple genes, including a set not previously implicated as miR-155 targets.

overall_design: Murine bone marrow cells transduced with Hoxa9-GFP + empty MIY vector were compared to Hoxa9+miR-155 and harvest for mRNA expression array. Three independent experiments were performed for each of the different conditions included in the study. Cells from were also transplanted into lethally irradiated mice to test for their transforming and leukemic potential.

first: Edith

last: Schneider

first: Anna

last: Staffas

first: Arefeh

last: Rouhi

first: Florian

last: Kuchenbauer


title: A unique pair of microarray datasets for microRNA profiling: data without careful design (Dataset B)

country: USA

summary: We set out to demonstrate the logistic feasibility of careful study design in microarray studies and the level of scientific benefits it can provide, in comparison with post-hoc data adjustment such as normalization, for the purpose of reducing the impact of handling effects on the accuracy and reproducibility of microarray data analysis. Towards this end, we conducted a study of microRNA expression using endometroid endometrial cancer tumors (n=96) and serous ovarian cancer tumors (n=96) that were all primary, untreated, and collected in 2000-2012 at Memorial Sloan Kettering Cancer Center. The same set of tumor tissue samples were profiled twice using the Agilent microRNA microarrays (Human miRNA V16.0), once with uniform handling and careful design for the allocation of arrays to samples and the second study without.

overall_design:
In the first study, arrays were assigned to tumor samples using blocked randomization and they were processed by one experienced technician in one single run. In the second study, arrays were assigned to tumor samples in the order of sample collection and they were handled by two technicians (the first of whom handled the first dataset) in multiple batches (with each batch on a separate date), mimicking typical practice. Dataset B is from the second study.
Tumor type: advanced serous ovarian cancer versus endometrioid endometrial cancer; batch: processing batches, Batch 1 to Batch 5.

first: Li

middle: X


title: mRNA microarray of Drosophila melanogaster extratced from cephalic complexes of lgl27S3/lglE2S31 (lgl-null) and FRT82B (wild-type) 3rd instar larvae

status: Public on Dec 18 2017

city: Tucson

first: Daniela

middle: C

last: Zarnescu

state: AZ

address: 1007 E Lowell St LSS 514

department: Molecular and Cellular Biology

institute: University of Arizona

summary:
Affymetrix microarray to detect changes in gene expression between lgl27S3/lglE2S31 and FRT82B larvae
4-day old 3rd instar lgl27S3/lglE2S31 larvae were compared to 0-day old 3rd instar FRT82B larvae

overall_design: RNA was isolated from 20 pairs of cephalic complexes per sample; samples were done in triplicate per condition but one FRT82B sample was not used due to QC issues

first: Scott

middle: G

last: Daniel

first: Atlantis

last: Russ


title: A unique pair of microarray datasets for microRNA profiling: data with careful design (Dataset A)

status: Public on Jan 08 2018

summary: We set out to demonstrate the logistic feasibility of careful study design in microarray studies and the level of scientific benefits it can provide, in comparison with post-hoc data adjustment such as normalization, for preventing confounding handling effects and improving the accuracy and reproducibility of disease-relevant biomarker detection. Towards this end, we conducted a study of microRNA expression using endometroid endometrial cancer tumors (n=96) and serous ovarian cancer tumors (n=96) that were all primary, untreated, and collected in 2000-2012 at Memorial Sloan Kettering Cancer Center. The same set of tumor tissue samples were profiled twice using the Agilent microRNA microarrays with different study designs.

overall_design:
In the first study, arrays were assigned to tumor samples using blocked randomization and they were processed by one experienced technician in one single run. In the second study, the arrays were assigned to the tumor samples in the order of their collection and they were handled by two technicians (the first of whom handled the first dataset) in five batches (with each batch on a separate date). This design mimicked typical practice. This dataset is from the first study.
Tumor type: advanced serous ovarian cancer or endometrioid endometrial cancer.


title: Genetic and bioinformatics approaches to decipher LGL's function as a tumor suppressor

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


title: Transcriptional data from yeast expressing mammalian AKT1

status: Public on Nov 30 2017

city: MADRID

first: Teresa

last: Fernandez-Acero

address: PLAZA DE RAMÓN Y CAJAL S/N

department: Departamento de Microbiología II

institute: Facultad de Farmacia UCM

summary: We studied the transcriptional profile in yeast cells in response to heterologous expression of mammalian activated AKT1

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: Three biological replicates of samples of yeast cells co-expressing for 4 hours mammalian catalytic subunit of class I PI3K and Akt (PI3K-AKT) or a kinase-dead (KD) version of Akt (PI3K-AKT K179M), and a microarray experiment was carried out for each sample.

first: Isabel

last: Rodriguez-Escudero

first: Víctor

last: J Cid

first: María

last: Molina


title: IAP proteins control polarization and immune-metabolism in committed macrophages

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

summary: Inhibitors of Apoptosis Proteins (IAPs) regulate apoptosis in response to various cellular assaults. Using both genetic and pharmacological approaches we demonstrate here that the IAPs not only support opportunistic survival of intracellular human pathogens like Chlamydia pneumoniae but also controls plasticity of iNOS+ M1 macrophage during the course of infection and render them refractory for immune stimulation. Treatment of Th1 primed macrophages with birinapant (IAP specific antagonist) inhibited NO generation and relevant proteins involved in innate immune signalling. Accordingly, birinapant promoted hypoxia, angiogenesis and tumor induced M2 polarization of iNOS+ M1 macrophages. Interestingly, birinapant driven changes in immune signaling was accompanied with changes in the expression of various proteins involved in the metabolism thus revealing the new role of IAP proteins on immune metabolic reprogramming in committed macrophages.

overall_design: Microarray experiments were performed as dual-color hybridizations on Agilent  4x44K Whole Mouse Genome Microarrays. To compensate for dye-specific effects, a dye-reversal color-swap was applied.

first: Vinod

last: Nadella

first: Aparna

last: Mohanty

first: Lalita

last: Sharma

first: Thomas

last: Rudel

first: Hridayesh

last: Prakash


title: Glis3 plays a crucial role in thyroid hormone production

status: Public on Nov 06 2017

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: The serum hormone levels including T3 and T4 were dramatically decreased in Glis3-null mice due to reduced production of thyroid hormones in thyroid. Gene expression profile and EdU incorporation analysis between WT and Glis3-null mice showed that the cell proliferation was greatly reduced in Glis3-null thyroid. Goitergenic diet (low iodine diet; LID) dramatically enhanced serum TSH levels in both WT and Glis3-null mice, however thyroid goiter was observed in WT mice but not in Glis3-null mice. A subset of genes associated with thyroid hormone production including Pendrin (Slc26a4), Nis (Na+/I– symporter, Slc5a5), Duoxa2 (dualoxidase A2), Tpo (thyroperoxidase), and Dio1 (Deiodinase1) was significantly induced in WT but not in Glis3-null mice by LID feeding.

overall_design: thyroid total RNAs were purified from 5 WT and 5 Glis3KO2 fed normal diet at 1 month old age, and 4 WT and 4 Glis3KO2 mice fed low iodine diet for 6 days. Then the samples were applied to Agilent mouse genome chip.

first: Hong

last: Kang

first: Anton

last: Jetten


title: Stromal R-Spondin orchestrates gastric epithelial homeostasis in health and disease

status: Public on Jun 30 2017

summary: Gastric epithelial stem cells are responsible for constant epithelial self-renewal, which is accelerated by infection with the gastric pathogen Helicobacter pylori. However, the mechanism that regulates stem cell turnover in the stomach remains unknown. Here we show that signaling by R-spondin 3 and Wnt hierarchically organizes the stem cell compartment in the antrum, producing two Wnt-responsive populations, which are either Lgr5+ve or Axin2 +ve. The positional identity of the Axin2+ve population relies on R-spondin 3 produced by stromal myofibroblasts. Increased availability of R-spondin induces hyperproliferation through specific expansion of Axin2+ve but not Lgr5+ve cells. Similarly, infection with H. pylori induces an increase in stromal R-spondin 3 expression, resulting in hyperplasia as well as shedding of bacteria that have entered the gland. This identifies a role for stromal cells in environmental sensing to orchestrate epithelial homeostasis via Wnt signaling.

overall_design:
Antral epithelial cells from R-spondin-treated mice and untreated control mice.
Microarray experiments were performed as dual-color hybridizations on Agilent whole mouse catalog 4x44K (Agilent-014868) arrays. To compensate for dye-specific effects, a dye-reversal color-swap was applied.

first: Michael

last: Sigal

first: Catriona

last: Logan

first: Hilmar

last: Berger

first: Bertram

last: Wiedenmann

first: Manuel

last: Amieva

last: Meyer

first: Hans

middle: J


title: Expression data of mouse transplantation for a novel standardized fold change (SFC) method

status: Public on Nov 18 2017

city: Ann Arbor

first: Weichen

last: Zhou

state: Michigan

address: 800 fuller St. 26

institute: Fudan University

summary: We used mouse transplantation data to evaluate the power of SFC method.Three case samples in the fifth day for cardiac transplantation were obtained. Three case samples in the fifth day and another three in the eighth day for liver transplantation were also obtained. We also designed control groups of three normal cardiac tissues and three hepatic tissues, respectively.Agilent Product Number: G4122F; Design ID: 014868.

overall_design: The cardiac transplantation was performed on the sex-matched B10 donor to the CBA recipient by microsurgical techniques. Three case samples in the fifth day were obtained. For orthotopic liver transplantation, grafts were harvested at POD5 or POD8 after transplantation and were submerged in RNAlater® stabilization solution (Life Technologies, Carlsbad, CA) for freezing. Total RNA was extracted from frozen tissue samples using ISOGEN (NipponGene, Tokyo, Japan). We also designed control groups of three normal cardiac tissues and three hepatic tissues, respectively.

first: W

first: M

last: Fujino

first: J

last: Wang

first: X

last: Li


title: Trancriptomic profiling of hepatocytes and mesenchymal cells of mice treated with phenobarbital for 2 weeks

status: Public on Jul 12 2017

city: Basel

first: Jonathan

last: Moggs

address: Fabrikstrasse 2

country: Switzerland

institute: Novartis

summary: Conventional notion regards the action of non-genotoxic carcinogens (NGC) an autonomous process largely confined to parenchymal cells. Here we aim to elucidate the role of the hepatic mesenchyme for the action of a prototypical NGC, phenobarbital (PB), an anti-epileptic drug.

overall_design: 12 weeks old male C57BL/6N mice received 50 mg/kg/day Phenobarbital for 14 days. We profiled mRNA expression in hepatocytes and mesenchymal cells to assess the different effects of treatment with phenobarbital on different liver tissues. Time-matched control animals received vehicle (H2O).

first: Teresa

last: Riegler

last: Römer

first: Bettina

last: Graup-Grasl


title: Post-transcriptional regulation of adult CNS axonal regeneration by Cpeb1

status: Public on Oct 01 2017

city: Heidelberg

first: Ana

last: Martin-Villalba

address: In Neuenheimer Feld 581

department: Molecular Neurobiology

institute: German Cancer Research Centre

summary:
Post-transcriptional regulation of gene expression plays important roles in neuron physiology, and likely do so as well in injury response of axons
We used microarray to profile expression changes in total and polysome-bound RNA upon spinal cord injury, to elucidate the role of post-transcriptional regulation towards axonal regeneration

overall_design: Mice were subjected to either a transection injury to the spinal cord or a sham operation. 9 hours post-operation, spinal cords were extracted. From this total RNA and polysome-bound RNA (isolated via sucrose gradient fractionation) were isolated and analyzed with Affymetrix microarrays

first: Stefan

last: Klussmann

first: Alvaro

last: Mateos


title: SIRT1 regulates methionine metabolism and pluripotency of mouse embrynoic stem cells (mESCs)

status: Public on Oct 10 2017

first: NIEHS

last: Microarray Core

summary: The goal of this project is to understand the role of SIRT1,  the most conserved mammalian NAD+-dependent protein deacetylase, in methionine metabolism and pluripotency of mESCs.  Our recent studies indicate that SIRT1 deficient mESCs are hypersensitive to methionine restriction-induced differentiation and apoptosis, primarily due to a reduced conversion of methionine to S-adenosylmethionine. This reduction leads to marked decrease in methylation levels of histones in SIRT1 deficient mESCs. To understand  the  impact of histone methylation alterations on stem cell functions in SIRT1 KO mESCs,  we examined the transcriptomes of SIRT1 WT and  KO mESCs cultured in either complete M10 medium (com) or methionine restricted medium containing 6 uM methionine (6met) for 6, 24, and 72 hours by microarray analysis.

overall_design: 3 groups of WT and SIRT1 KO mESCs were cultured in the complete medium (com) or methioine restricted medium (6met) for 6, 24, or 72 hours. Cells were then harvested and total RNA was isolated using the Qiagen RNeasy mini-kit. Gene expression profiles were analyzed using Agilent Whole Mouse Genome 4x44 multiplex format oligo arrays (014868) (Agilent Technologies, Santa Clara, CA), following the Agilent 1-color microarray-based gene expression analysis protocol.

first: Xiaoling


title: Integrated in vivo multiomics analysis identifies p21-activated kinase signaling as a driver of colitis

status: Public on Jun 16 2017

city: CAMBRIDGE

first: Jesse

last: Lyons

state: Ma

address: 77 Massachusetts Ave 16-343

department: Bioengineering

institute: Massachusetts Institute of Technology

summary:
Background and aims: To gain insight into the pathogenesis of chronic colonic inflammation (colitis), we performed a multi-omic analysis that integrates RNA microarray, total protein mass spectrometry, and phospho-protein measurements from a mouse model. We used this multi-dimensional dataset to track information flow from RNA to protein to phospho-protein and to ascertain which facets of inflammation are described by each data stream. Using trans-omic co-expression network analysis, we find that there are distinct modes of regulation present in the conserved and divergent correlation structures of the three data streams. As a result, each data stream provides a unique viewpoint on the molecular pathogenesis of colitis. Nevertheless, multiple independent computational analyses identified increased signaling through p21-activated kinase (Pak) during colitis, and chemical inhibition of Pak1/2 suppressed inflammation in mice.  These studies provide a comprehensive view of the state of signaling in the context of colitis and identify Pak as a therapeutic target.
We used microarrays to examine changes in global gene expression patterns associated with chronic inflammation induced by the T cell transfer model of Inflammatory Bowel Disease.

overall_design: Rag1 knockout mice were injected with inflammation-inducing Naïve T cells or, as a negative control, regulatory T cells. Animals were sacrificed when they showed signs of severe inflammation (weight loss, diarrhea). Colons were opened longitudinally and a thin strip of tissue was excised and snap frozen from the cecum to the rectum. This experiment includes data from 5 control animals and 3 severely inflamed animals.

first: Douglas

last: Brubaker

first: Katherine

last: Baldwin

first: Amanda

last: Edwards

first: Myriam

last: Boukhali

first: Samantha

middle: D

last: Strasser

first: Yi-Jang

last: Lin

first: Vijay

last: Yajnik

first: Joseph

last: Kissil

first: Wilhelm

last: Haas

last: Lauffenburger

first: Kevin

last: Haigis

first: Phaedra

last: Ghazi

first: Lucia

last: Suarez-Lopez


title: An embryonic system to assess Wnt transcriptional targets:  Comparing opposing Wnt pathways and transcriptional activation and repression.

status: Public on Aug 28 2017

city: Cardiff

first: NATHAN

last: HARMSTON

address: Museum Avenue

institute: Cardiff University

summary: During animal development, signals determine and organize a vast number of complex tissues using a very small number of signal transduction pathways. These developmental signaling pathways determine cell fates through a coordinated transcriptional response that remains poorly understood. The Wnt pathway is involved in a variety of these cellular functions, and its signals are transmitted in part through a β-catenin/TCF transcriptional complex. Here we report an in vivo Drosophila assay that we used to distinguish between activation, de-repression and repression of transcriptional responses, separating upstream and downstream pathway activation and canonical/non-canonical Wnt signals in embryos. We find a specific set of genes downstream of both β-catenin and TCF with an additional group of genes regulated by Wnt. The non-canonical Wnt4 regulates a separate cohort of genes. We correlate transcriptional changes with phenotypic outcomes of cell differentiation and embryo size, showing our model can be used to characterize developmental signaling compartmentalization in vivo.

overall_design: 2 replicates per condition

first: Nathan

last: Harmston

first: Nicholas

last: Tolwinski


title: Effect of Rag1 mutation on kidney immune response

status: Public on Jun 12 2017

city: Leiden

first: Monica

last: Varela

address: Einsteinweg 55

department: ASH

institute: Leiden University

summary: We used Rag1 mutant fish vs Wild type fish to analyze the kidney transcriptomic modulation and determine how the mutation affects the general gene transcription (without stimuli) in fish, but also the immune response against Poly I:C.

overall_design: Healthy 1 year old fish (Wild type and Rag1-/- mutants) were intraperitoneally injected with 10 µg of pure Poly I:C (Sigma) or PBS. Per biological replicate, kidneys from 4 fish were sampled and pooled at 24 hours post injection (the dataset contains 4 biological replicates)

first: Gabriel

last: Forn-Cuní

first: Sonia

last: Dios

first: Antonio

last: Figueras

first: Beatriz

last: Novoa


title: FGF18 Signaling for Hair Cycle Resting Phase Determines Radioresistance of Hair Follicles by the Arrest of Hair Cycling

status: Public on Jun 03 2017

city: Chiba

first: Atsuko

last: Ishikawa

state: Chiba

address: Anagawa 4-9-1

department: Research Center for Charged Particle Therapy

institute: National Institute of Radiologocal Sciences

summary: Telogen (resting phase) hair follicles are more radioresistant than anagen (growth phase) ones. Irradiation of BALB/c mice in the anagen phase with γ-rays at 6 Gy induced hair follicle dystrophy, whereas irradiation in the telogen phase induced the arrest of hair follicle elongation without any dystrophy after post-irradiation depilation. In contrast, FGF18 was highly expressed in the telogen hair follicles to maintain the telogen phase and also the quiescence of hair follicle stem cells. Therefore, the inhibition of FGF receptor signaling at telogen induced the dystrophy after post-irradiation depilation. In addition, the administration of recombinant FGF18 suppressed cell proliferation in the hair follicles and enhanced the repair of radiation-induced DNA damage, so FGF18 protected the anagen hair follicles against radiation damage to enhance hair regeneration. Moreover, FGF18 reduced the expression of cyclin B1 and cdc2 in the skin and FGF18 signaling induced G2/M arrest in the keratinocyte cell line HaCaT, although no obvious change of the expression of DNA repair genes was detected by DNA microarray analysis. These findings suggest that FGF18 signaling for the hair cycle resting phase causes radioresistance in telogen hair follicles by arresting the proliferation of hair follicle cells.

overall_design: Portions of dorsal skin of 7-week-old male BALB/c mice were depilated to induce anagen phase of hair follicles. One hundred micrograms of FGF18 diluted in saline containing 5 μg/μl heparin was administered intraperitoneally to mice 6 days after depilation, and then mice were subjected to total body irradiation with γ-rays at 6 Gy 24 h after FGF administration. The skin was removed from treated mice 4 h after irradiation and total RNAs were isolated from the skin. The mRNA expression profiles were obtained using Affymetrix GeneChip Mouse Gene 2.0 ST Array (Affymetrix, Santa Clara, CA, USA).

first: Fumiaki

last: Nakayama

first: Sachiko

last: Umeda

first: Takeshi

last: Yasuda

first: Mitsuko

last: Kawano

first: Mayumi

last: Fujita

first: Toru

last: Imamura

first: Takashi

last: Imai


title: FGF18 affects hair cycle.

status: Public on May 15 2017

city: Tsukuba

first: Myco

last: Umemura

state: Ibaraki

address: Higashi 1-1-1

department: Bioproduction Research Institute

institute: National Institute of Advanced Industrial Science and Technology (AIST)

summary: Fgf18 gene is strongly expressed in hair follicles of mouse dorsal skin during regressing (catagen) and resting (telogen) phases of hair cycle, but not in growth (anagen) phase.  This study aims at identifying the effects of FGF18 local delivery on the anagen phase of hair cycle.

overall_design: To define genes affected by local delivery of FGF18 during anagen phase of hair cycle, we injected FGF18 protein subcutaneously into back skin of C3H/HeN mice on day 4 of depilation-induced anagen. As control PBS was injected in place of FGF18. After 24 h (61-d-old), total RNA was isolated from the back skin and purified to poly A RNA. The RNA samples were pooled for each group. Gene expression was analyzed by one-color analysis using single array for each group.

first: Miho

last: Kimura-Ueki


title: Global gene expression analysis highlights microgravity sensitive key genes in longissimus dorsi and tongue of 30 days space-flown mice

status: Public on May 23 2017

first: Dieter

last: Blottner

address: Phillipstrasse 12

department: Anatomy

institute: Charité Universitaetsmedizin Berlin

summary: Microgravity as well as chronic muscle disuse are two causes of low back pain originated at least in part from paraspinal muscle deconditioning. At present no study investigated the complexity of the molecular changes in human or mouse paraspinal muscles exposed to microgravity. The aim of this study was to evaluate longissimus dorsi and tongue (as a new potential in-flight negative control) adaptation to microgravity at global gene expression level. C57BL/N6 male mice were flown aboard the BION-M1 biosatellite for 30 days (BF) or housed in a replicate flight habitat on ground (BG). . Global gene expression analysis identified 89 transcripts differentially regulated in longissimus dorsi of BF vs. BG mice (False Discovery Rrate < 0,05 and fold change < -2 and > +2), while only a small number of genes were found differentially regulated in tongue muscle ( BF vs. BG = 27 genes).

overall_design: C57BL/N6 mice were randomly divided in 3 groups: Bion Flown (BF), mice flown aboard the Bion M1 biosatellite in microgravity environment for 30 days; Bion Ground (BG), mice housed in the same habitat of flown animals but exposed to earth gravity; and Flight Control (FC), mice housed in a standard animal facility.

first: Guido

last: Gambara

first: Michele

last: Salanova

first: Ute

last: Ungethüm


title: Fgf18 regulates hair cycle

summary: Fgf18 gene is strongly expressed in hair follicles of mouse dorsal skin during regressing (catagen) and resting (telogen) phases of hair cycle, but not in growth (anagen) phase.  This study aims at identifying the function of Fgf18 in the regulation of hair cycle.

overall_design: To define target genes of Fgf18 during telogen phase of hair cycle, we generated mice in which Fgf18 gene is conditionally knocked out in keratin 5-positive epithelial cells (referred to as Fgf18 cKO below). We carried out microarray experiments with mouse back skin samples harboring telogen hair follicles obtained from three 42-d-old Fgf18 cKO male mice, or from three 42-d-old C57BL/6 male mice as control.  Total RNA was isolated from each mouse and further purified to polyA RNA using oligo dT30 columns.  The RNA samples were pooled for each group. Gene expression was analyzed by one-color analysis using duplicate arrays for each group.


title: Brg1 enables rapid growth of the early embryo by suppressing genes that regulate apoptosis and cell growth arrest

status: Public on Apr 21 2017

first: NIEHS

last: Microarray Core

summary: Global gene expression analysis revealed that genes up regulated in Rosa26CreERTM; Brg1floxed/floxed embryos (Rosa26CreERTM; Brg1floxed/floxed hereafter referred as Brg1d/d that is designated for deleted Brg1floxed/floxed alleles in embryos) negatively regulate cell cycle progression, and cell growth.

overall_design: RNA from Brg1floxed/floxed (wild type control) Day 8.5 embryos (three biological replications) and RNA from Brg1d/d (Brg1 CKO: conditional knockout) Day 8.5 embryos (three biological replications) were used for global gene expression analysis.

first: Ajeet

last: Singh

first: Julie

middle: F

last: Foley

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