title: Differentiation analysis of Mouse Posterior Neural tube

status: Public on Mar 05 2018

city: Boston

first: Jerome

last: Chal

state: MA

address: 77 ave Louis Pasteur

institute: Brigham and Women's Hospital

summary: Posterior embryonic axis develops from neuromesodermal progenitors which differentiate into neural tube and paraxial mesoderm

overall_design: Neural tube (NT) were dissected into 6 pieces in Stage E9.5 Mouse embryo. The experiment was designed to have biological duplicate in each pieces. Neural Tube was taken from 2 embryos to generate this dataset

first: Masayuki

last: Oginuma

first: Philippe

last: Moncuquet


title: Impact of bariatric surgery on placental transcriptome

status: Public on Mar 01 2018

city: Jackson

first: Michael

middle: R

last: Garrett

state: MS

address: 2500 North State Street

department: Pharmacology

country: USA

institute: University of Mississippi Medical Center

summary: In the present study, we sought to understand the impact of bariatric surgery [using vertical sleeve gastrectomy (VSG)] on transcriptome changes in the placenta . Female Adult,  Long Evans were fed high fat diet (HFD, #D03082706, Research Diets) for 4 weeks, divided into sham-VSG or VSG groups, and following surgeries one group of sham-VSG and VSG were switched to normal diet (lean), while one sham-VSG group (obese) continued HFD. At gestdational day 18, placenta tissues harvested from  pregnant female rats were processed for Affymetrix microarray and  transcriptomic analysis performed.

overall_design: Three groups of animals: lean sham-VSG (n=6), obese shame-VSG (n=6), and VSG (n=6)

first: Bernadette

last: Grayson


title: Expression data from Germ-Free (GF) and L.NK2-colonized mice intestinal epithelial cells and Peyer's patches cells

city: Tianjin

first: Rongcun

last: Yang

address: Weijin Road 94

department: Immunology

country: China

institute: Nankai university

summary:
Lactobacillus NK2 (L.NK2) is a commensal microbe, isolated from the mouse intestinal feces in our lab. To examine the potential role of L. NK2 in the gut immunity, we monocolonized GF mice with L.NK2. And, we conducted a microarray experiment to compare the transcriptomes of GF and L.NK2-colonized mice intestines under the same experimental condition
We used microarrays to detail the global programme of gene expression in intestinal epithelial cells (IEC) and Peyer's patches cells (PP) of GF and L.NK2-colonized mice.

overall_design: GF mice monocolonized with 1*10^8 L.NK2, two weeks later, IEC and PP of GF and L.NK2-colonized mice of the same physiological and maintaining condition were isolated and then total RNAs were extracted from them, which could reflect the respective transcription profile of GF and L.NK2-colonized mice. These RNAs were detected by microarray and the influence of L.NK2 on intestine could be revealed to some extent.


title: Expression data from HEK 293T cells overexpressing either myc-FUS or myc-R495X

status: Public on Mar 14 2018

city: Baltimore

first: Jiou

last: Wang

state: MD

address: 615 N. Wolfe St.

institute: Johns Hopkins University

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

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

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: RNA-seq analysis of IL-1B and IL-36 responses in epidermal keratinocytes identifies a shared MyD88-dependent gene signature

status: Public on Mar 04 2018

city: Ann Arbor

first: William

last: Swindell

state: MI

address: 1500 E. Medical Center Drive

department: Dermatology

institute: University of Michigan

type: Expression profiling by high throughput sequencing

summary: IL-36 cytokines have recently emerged as mediators of inflammation in autoimmune conditions including psoriasis vulgaris (PsV) and generalized pustular psoriasis (GPP). This study used RNA-seq to profile the transcriptome of primary epidermal keratinocytes (KCs) treated with IL-1B, IL-36A, IL-36B or IL-36G. We identified some early IL-1B-specific responses (8 hours post-treatment), but nearly all late IL-1B responses were replicated by IL-36 cytokines (24 hours post-treatment). Type I and II interferon genes exhibited time-dependent response patterns, with early induction (8 hours) followed by no response or repression (24 hours). Altogether, we identified 225 differentially expressed genes (DEGs) with shared responses to all 4 cytokines at both time points (8 + 24 hours). These involved up-regulation of ligands (IL1A, IL1B, IL36G) and activating proteases (CTSS), but also up-regulation of inhibitors such as IL1RN and IL36RN. Shared IL-1B/IL-36 DEGs overlapped significantly with genes altered in PsV and GPP skin lesions, as well as genes near GWAS loci linked to autoimmune and autoinflammatory diseases (e.g., PsV, psoriatic arthritis, IBD, primary biliary cholangitis). Inactivation of MyD88 adapter protein using CRISPR/Cas9 completely abolished expression responses of such DEGs to IL-1B and IL-36G stimulation. These results provide a global view of IL-1B and IL-36 expression responses in epidermal KCs with fine-scale characterization of time-dependent and cytokine-specific response patterns. Our findings support an important role for IL-1B and IL-36 in autoimmune or autoinflammatory conditions and show that MyD88 adaptor protein mediates shared IL-1B/IL-36 responses.

overall_design: Cultures were treated with truncated recombinant human IL-1B, IL-36A, IL-36B or IL-36G (10 ng/ml for IL-1B; 2000 ng/ml for IL-36 cytokines). Three cell lines were used (lines A, B and C) with samples processed in 4 batches. Samples within the same batch are comparable. Experiments were performed with 8 and 24 hours of cytokine treatment (n = 2-3 per time point).

first: Johann

middle: E

last: Gudjonsson


title: Expression data from HEK 293T cells overexpressing either myc-FUS or myc-R495X (exon)

summary:
Individuals with the ALS-linked (amyotrophic lateral sclerosis) truncation mutation (R495X) in FUS (fused in sarcoma) are known to have a more aggressive form of the disease than those with point mutations.  The underlying cause for this difference is unclear.  We report that FUS is a component of miRISC (miRNA-induced silencing complex) and that overexpression of its truncation mutant R495X negatively impacts miRNA mediated RNA silencing.
In this study, we compared the impact overexpression of wild-type myc-tagged FUS versus truncation mutant R495X has on global gene expression.

overall_design: Pairwise comparisons were made based on three biological replicates from two groups: 293Ts expressing myc-tagged R495x versus those expressing wild-type myc-tagged FUS.

first: P

middle: M

last: Mullane


title: Different expression profiles of lncRNAs, mRNAs and circRNAs in preeclampsia and normal placenta  None

city: Beijing

first: Zhenyu

last: Zhang

address: Gongtinanlu 8hao

institute: Beijing Chao-Yang Hospital,Capital Medical University


title: Cancer-associated rs6983267 SNP and its accompanying long non-coding RNA CCAT2 induce myeloid malignancies via unique SNP-specific RNA mutations

status: Public on Feb 28 2018

city: Houston

first: George

last: Calin

state: TX

address: 1881 East Road

department: Experimental Therapeutics

institute: MD Anderson Cancer Center

summary:
The cancer-risk associated rs6983267 single nucleotide polymorphism (SNP) and the accompanying long non-coding RNA CCAT2 in the highly amplified 8q24.21 region has been implicated in cancer predisposition, though causality has not been established. Here, using allele-specific CCAT2 transgenic mice, we demonstrate that CCAT2 overexpression leads to spontaneous myeloid malignancies. CCAT2 is overexpressed in bone marrow and peripheral blood of myelodysplastic/myeloproliferative neoplasms (MDS/MPN) patients. CCAT2 induces global deregulation of gene expression by downregulating EZH2 in vitro and in vivo in an allele-specific manner. We also identified a novel disease-specific RNA mutation (named DNA-to-RNA allelic imbalance, DRAI) at the SNP locus in MDS/MPN patients and CCAT2-transgenic mice.  The RNA transcribed from the SNP locus in malignant hematopoietic cells have different allelic composition from the corresponding genomic DNA, a phenomenon rarely observed in normal cells. Our findings provide fundamental insights into the functional role of rs6983267 SNP and CCAT2 in myeloid malignancies.
We performed genome-wide microarray expression profiling to study the genetic landscape alterations induced by CCAT2 and DRAI

overall_design: Bone marrow cells of WT mice (n = 4), CCAT2-G and CCAT2-T mice (DRAI- group, n = 8) and CCAT2-GT mice (DRAI+ group, n = 6) were used for the analysis.

middle: A

first: Maitri

middle: Y

last: Shah


title: Endogenous retrovirus-associated genes in a hypoxia-mimetic cobalt chloride neuroblastoma model

status: Public on Mar 07 2018

city: Halle (Saale)

first: Martin

middle: Sebastian

last: Staege

state: Sachsen-Anhalt

address: Ernst-Grube-Str. 40

department: Universitätsklinik u. Poliklinik für Kinder- u. Jugendmedizin

country: Germany

summary: By using high-density DNA microarrays, we analyzed the gene-expression profile of SHSY5Y neuroblastoma cells after treatment with cobalt chloride

overall_design: RNA was extracted from SHSY5Y cells after treatment with 0, 100, or 200 µM cobalt chloride and analyzed with Affymetrix Human Exon 1.0ST microarrays.

first: Stefanie

last: Brütting

first: Harini

last: Narasimhan

first: Frank

last: Hoffmann

first: Malte

last: Kornhuber

middle: S

first: Alexander

last: Emmer


title: How can ant queens live so long? Genes of multiple longevity pathways change expression with age in the ant Temnothorax rugatulus

status: Public on Mar 06 2018

city: Mainz

first: Matteo

middle: Antoine

last: Negroni

address: Joh.-von-Müller-Weg 6 Room 02-239

department: Institute of Organismic and Molecular Evolution

institute: Johannes Gutenberg, University, Mainz

summary: Senescence is manifested by an increase in oxidative stress and a decline in biological functions with age. In most organisms, body maintenance is traded-off with reproduction. The negative relationship between longevity and fecundity is also evident on the molecular level, yet the proximate mechanisms remain poorly understood. Apparently by-passing this trade-off, social insect queens are both extremely long-lived (up to 30 years in some ants) and highly fecund compared to workers. Here, we study changes in gene expression with age and fecundity in queens to determine how the trade-off between those two traits is reshaped. We analyse tissue-specific gene expression in young founding queens and old, highly fecund queens of the ant Temnothorax rugatulus. More genes altered their expression with age in the fat body than in the brain. Despite strong differences in ovary development, few fecundity genes were differentially expressed. However, many longevity genes involved in well-known pathways or lifespan-associated biological processes changed their expression with age indicating that multiple longevity mechanisms are activated successively throughout a queens’ life. Young queens invested in immunity (i.e. activation of the Toll signalling pathway) and resistance against environmental and physiological stress associated with the founding phase (i.e. down regulation of the TOR pathway), while established older queens up-regulate anti-aging mechanisms (i.e. up-regulation of catalase, superoxide dismutase, heat shock 70 kDa proteins). Finally, we identified a number of candidate genes and pathways, potentially involved in reshaping the fertility-longevity trade-off in social insects, shedding light on how this is achieved on a proximate level.

overall_design: We did a comparative study by comparing tissue specific gene expression in the brain and the fat body between 8 old and 8 young queens. Those 16 queens were collected in the field

first: Susanne

last: Foitzik

first: Barbara

last: Feldmeyer


title: Gene expression of cardiac fibroblasts post-MI

status: Public on Feb 24 2018

city: Cincinnati

first: Vikram

last: Prasad

state: OH

address: 240, Albert Sabin Way

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

summary:
Cardiac fibroblasts stay relatively quiescent under normal condition. These cells differentiate to myofibroblasts after myocardial infarction (MI), characterized by the expression of contractile proteins and secretion of elevated levels of extracellular matrix proteins, leading to cardiac remodeling. The differentiated myofiroblasts gradually lose most myofibroblast phenotypes but still persist in the infarct area to maintain the tissue structural integrity.
We used microarrays to reveal the change in cardiac fibroblast gene expression profile after MI.

overall_design: TCF21 lineage-traced cardiac fibroblasts were isolated from left ventricle by FACS before, and 3 days, 7 days, 2 weeks, and 4 weeks post-MI for RNA extraction and Affymetrix microarrays.

first: Xing

last: Fu

first: Jeffery

last: Molkentin


title: Expression data from hippocampus of Phf8 knock out and wild type mice

status: Public on Feb 23 2018

city: Shanghai

first: Xuemei

last: Chen

address: 320 Yueyang Road

department: State Key Laboratory of Molecular Biology

institute: Chinese Academy of Sciences

summary:
We used microarrays to detail the global programme gene expression of Phf8 knock out and wild type mice
Different expression profile were compared between Phf8 knock out and wild type mice

overall_design: Hippocampus tissue from Phf8 knock out and wild type mice were isolated for RNA extraction and hybridization on Affymetrix microarrays，and compared the difference between the two groups

first: Chen

last: Xuemei

first: Yu

last: lu


title: The lateral cerebellum is preferentially sensitive to high sonic hedgehog signaling and medulloblastoma formation

status: Public on Feb 22 2018

city: New York

first: Alexandra

last: Joyner

state: NY

department: Developmental Biology

institute: Sloan Kettering Institute

summary: The main cell of origin of the Sonic hedgehog (SHH) subgroup of medulloblastoma (MB) is granule cell precursors (GCPs), a SHH-dependent transient amplifying population in the developing cerebellum. SHH-MBs can be further subdivided based on molecular and clinical parameters, as well as location since SHH-MBs occur preferentially in the lateral cerebellum (hemispheres). Our analysis of adult patient data suggests that tumors with Smoothened (SMO) mutations form more specifically in the hemispheres than those with Patched 1 (PTCH1) mutations. Using sporadic mouse models of SHH-MB with the two mutations commonly seen in adult MB, constitutive activation of Smo (SmoM2) or loss-of-Ptch1, we found that regardless of timing of induction or type of mutation, tumors developed primarily in the hemispheres with SmoM2-mutants indeed showing a stronger specificity. We further uncovered that GCPs in the hemispheres are more susceptible to high level SHH signaling compared to GCPs in the medial cerebellum (vermis), as more SmoM2 or Ptch1-mutant hemisphere cells remain undifferentiated and show increased tumorigenicity when transplanted. Finally, we identified location-specific GCP gene expression profiles, and found that deletion of the genes most highly expressed in the hemispheres (Nr2f2) or vermis (Engrailed1) showed opposing effects on GCP differentiation. Our studies thus provide new insights into intrinsic differences within GCPs that impact on SHH-MB progression.

overall_design: The P8 wild type GCPs or SmoM2-mutant GCPs (Atoh1-CreER/+; R26LSL-SmoM2-YFP; 200ug/g Tm at P2) from either cerebellar hemispheres or vermis were isolated by Percoll gradient. 5 mice were pooled for each replicate. The MSKCC Integrated Genomics Operation (IGO) core facility performed RNA isolation and microarray analysis. Briefly, high quality RNA were interrogated with Affymetrix microarrays (GeneChip™ Mouse Genome 430 2.0 Array). GeneChip CEL files were analyzed with the Partek Genomics Suite and Gene Pattern, including unsupervised hierarchical clustering strategies and PCA. Supervised analyses comprised LIMMA, ANOVA, and SAM to infer specific genesets

middle: L

first: Alexandre

last: Wojcinski

first: I-Li

last: Tan

first: Marc

last: Remke


title: MLE12 cell transcriptome analysis 12, 24, 48h after Notch 1-ICD overexpression with NICD1-pIRES-dsRed2 vector

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

institute: Justus-Liebig University Giessen

summary: To study the effect of Notch 1 overexpression on cell funtion and to elucidate involved signalling pathways MLE12 cells tranfected with NICD1-pIRES-dsRed2 vector were analyzed for their transcript profiles 12, 24, and 48h after transfection and related to an empty vector (EV) transfected control cells

overall_design: Balanced dye-swap dual-color hybridizations of 6-7 independent replicates per time-point. On each array, RNA from Notch-1 overexpressing cells and from control cells (empty vector transfected) for the same time-point were hybridized.

first: Clemens

last: Ruppert


title: Gene expression data from colorectal cancers

status: Public on Feb 14 2018

city: Dunedin

first: Sunali

last: Mehta

state: Otago

address: 56 Hanover Street, Dunedin

country: New Zealand

institute: University of Otago

summary:
D122p53 mice (a model of D133p53 isoform) are tumour prone, have extensive inflammation and elevated serum IL-6. To investigate the role of IL-6 we crossed ∆122p53 mice with IL-6 deficient mice. Here we show that loss of IL-6 reduced JAK-STAT signalling, tumour incidence, and metastasis. We also show that D122p53 activates RhoA-ROCK signalling leading to tumour cell invasion which is IL-6 dependent and can be reduced by inhibition of JAK-STAT and RhoA-ROCK pathways. Similarly, we show that Δ133p53 activates the these pathways, resulting in invasive and migratory phenotypes, in colorectal cancer cells. Gene expression analysis of colorectal tumours showed enrichment of GPCR signalling associated with D133TP53 mRNA. Patients with elevated D133TP53 mRNA levels had a shorter disease free survival. Our results suggest that D133p53 promotes tumour invasion by activation of the JAK-STAT and RhoA-ROCK pathways and that patients whose tumours have high D133p53 may benefit from therapies targeting these pathways.
In this dataset, we included the gene expression data from 35 colorectal cancers. These data were used to identify a list of enriched genesets associated with D133TP53 mRNA expression in colorectal tumours

overall_design: D133TP53 mRNA expression determined by RT-qPCR was combined with transcript level data from Affymetrix Human Exon 1.0 ST arrays for the 35 colorectal tumours. Using Spearman's correlation analyses we identified D133TP53 mRNA was associated with the expression of 364 genes (Spearman’s correlation coefficient r ≥ 0.35). Enrichment of gene sets within the input list was determined using the overrepresentation test with default settings using Bonferroni correction in Pantherdb

first: Hamish

last: Campbell

first: Nicholas

last: Fleming

first: Imogen

last: Roth

last: Metha

first: Anna

last: Wiles

first: Gail

last: Williams

first: Claire

last: Vennin

first: Nikola

last: Arsic

first: Ashleigh

last: Morghan

first: Marina

last: Pajic

first: Fran

last: Munro

first: Les

last: McNoe

first: Michael

last: Black

first: John

last: McCall

first: Tania

last: Slatter

first: Paul

last: Timpson

first: Roger

last: Reddel

first: Pierre

last: Roux

first: Cristin

last: Print

first: Margaret

last: Baird

first: Antony

middle: W

last: Braithwaite


title: HER2 Overexpression Modifies the Cellular Response to Hypoxia in MCF7 Breast Cancer Cell Lines

city: Edinburgh

first: Edward

middle: Joseph

last: Jarman

address: Crewe Road south

department: Institute of Genetics and Molecular Medicine

country: United Kingdom

institute: University of Edinburgh

summary: Tumour hypoxia is a recognised driver of breast cancer pathology. The main cellular response to hypoxia is mediated by the hypoxia-inducible factors HIF1 and HIF2, and is controlled through the regulation of oxygen-labile HIFα subunits. HIF1α has a well-established role in breast cancer where it has also been shown to be regulated by growth factor signalling. However, the role of HIF2α has been less thoroughly researched. Here, the role of HIF2α was investigated in breast cancer cell lines and publicly available gene expression datasets to determine its relationship with HER2 receptor expression in breast cancer. Using an isogenic cell line model for HER2 overexpression, we establish a direct role for HER2 in driving HIF2α expression in breast cancer. The effect of HER2-mediated HIF2α expression on the cellular response to acute and chronic hypoxia was investigated in 2D and 3D cell line models, and through protein and gene expression analysis, HER2 was shown to drive an exacerbated hypoxic response in these cells. In growth assays, HER2-overexpressing cell lines were shown to be highly sensitive to HIF2-specific inhibition through HIF2α-targeted siRNA and treatment with the HIF2α-specific translation inhibitor C76. Additionally, survival analysis in a large, publicly available dataset demonstrated a relationship between HIF2α and poor disease-specific survival in HER2-overexpressing tumours. We demonstrate a novel role for HIF2α in driving an increased hypoxic response in breast cancer cells and suggest HIF2 signalling may be an important, targetable pathway in HER2-positive breast cancers.

overall_design: Total RNA was obtained from MCF7 and MCF7-HER2 cells grown in normoxia (20% O2), or hypoxia (0.5% O2) for 24 hours (acute) or for 10 weeks (chronic). Each sample had n=3 replicates.

middle: J


title: Treatment of 3T3-L1 adipose cells with Glucose Oxidase

city: Camperdown, Sydney

first: Rima

last: Chaudhuri

state: NSW

address: D17 Johns Hopkins Drive

department: Charles Perkins Center

country: Australia

institute: University of Sydney

summary: 3T3-L1 adipose cells were grown, differentiated and insulin resistance was stimulated by addition of Glucose Oxidase.

overall_design: Gene expression in 3T3-L1 cells control cells and during treatment with Glucose oxidase 3 samples per group serve as experimental replicates.

first: Zora

last: Modrusan


summary: MnTBAP reversed insulin resistance without significant alteration to gene expression

overall_design: Treatment of insulin resistant 3T3-L1 adipose cells with MnTBAP. The experimental design is reported in PMID 19805130.


title: Gene expression changes in stimulated and unstimulated Foxp1-deficient B cells.

status: Public on Feb 19 2018

city: Munich

first: Silvia

last: Thoene

address: Ismaninger Str. 22

institute: Klinikum rechts der Isar der TUM

summary:
Foxp1 is expressed throughout B cell development, but the physiological functions in mature B lymphocytes are unknown. We therefore evaluated differential gene expression in Foxp1-deficient B cells, with or
withouth IgM stimulation.

overall_design: B220+ B cells from Foxp1flox/del or Foxp1wt/flox mice were isolated by FACS. Cells were left untreated or stimulated with IgM for four hours before RNA isolation.

first: Thomas

last: Patzelt

first: Jürgen

last: Ruland


title: Expression data from cells at reprogramming day 3, 5 and 7

first: BING

last: LIAO

address: 227，South Chongqing Road

institute: Shanghai Jiao Tong University School of Medicine

summary:
The protein level of OCT4, a core pluripotency transcriptional factor, is vital for embryonic stem cell (ESC) maintenance, differentiation and somatic cell reprogramming. Although OCT4 protein is regulated at multiple scales, the role and regulatory mechanisms of OCT4 ubiquitination in reprogramming remains elusive. We identified the five lysine residues as ubiquitination sites on OCT4, and found that destruction of the ubiquitination can enhance OCT4 activity in reprogramming.
We used microarrays to detail the global  gene expression underlying cellular reprogramming induced by two sets of reprogramming factor combinations, including O(WT)SK and O(5R)SK, and identified distinct pattern of gene expression change  during this process.

overall_design: Reprogramming cells, induced by transcription factor combination of O(WT)SK or O(5R)SK, were collected at successive stages at day 3, 5, and 7 for RNA extraction and hybridization on Affymetrix microarrays.

first: Bing

last: Liao

first: Ying

last: Jin


title: MNase-Seq for budding yeast Saccharomyces cerevisiae

status: Public on Feb 16 2018

city: Kashiwa

first: Fumihito

last: Miura

state: Chiba

address: Kashiwanoha 5-1-5

department: Graduate School of Frontier Sciences

country: Japan

institute: The University of Tokyo

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Libraries were prepared by using two methods. The one is ThruPlex kit from Rubicon Genomics, the other is TCS-ligation based method described in our paper.

overall_design: Two methods for preparation of next-generation sequencing libraries were compared.


title: Wildtype and NRP1 knockout macrophages

status: Public on Feb 11 2018

city: Montreal

first: Przemyslaw

last: Sapieha

state: Quebec

address: 5345 Assumption Blvd

country: Canada

institute: Maisonneuve-Rosemont Research Center

summary: Obesity gives rise to metabolic complications by mechanisms that are poorly understood. While chronic inflammatory signaling in adipose tissue is typically associated with metabolic deficiencies linked to excessive weight gain, we identified a subset of NRP1-expressing myeloid cells that accumulate in adipose tissue and protect against obesity and metabolic syndrome. Ablation of NRP1 in macrophages compromised lipid uptake in these cells, which reduced substrates for fatty acid β-oxidation and shifted energy metabolism of these macrophages towards a more inflammatory glycolytic metabolism. Conditional deletion of NRP1 in LysM Cre-expressing cells lead to inadequate adipose vascularization, accelerated weight gain and reduced insulin sensitivity even independent of weight gain. Transfer of NRP1+ hematopoietic cells improved glucose homeostasis, resulting in the reversal of a prediabetic phenotype. Our findings suggest a pivotal role for adipose tissue resident NRP1+-expressing macrophages in driving healthy weight gain and maintaining glucose tolerance.

overall_design:
2 samples were analyzed: wildtype macrophages (3 replicates), and NRP1 deficient macrophages (2 replicates)

Raw data available only for sample GSM2991368 (Wildtype 3).

first: Ariel

last: Wilson


title: Gene expression profiles in pairs of synchronous and metachronous bilateral breast tumors and primaries and their local recurrences

status: Public on Feb 13 2018

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

country: Italy

institute: IRCCS Ospedale San Raffaele

summary: Dissecting time-related from genetic-related gene expression variability in the bilateral breast cancer model.

overall_design: We investigated gene expression variations within three sets of paired samples, including 18 Synchronous Bilateral Cancer, 11 Metachronous Bilateral Cancer and 10 Local Recurrence Cancer, in women with negative lymph nodes which have been subjected to loco-regional treatment only.

first: Maria

middle: G

last: Daidone


title: Expression data from mouse lung squamous cell carcinoma isolated from KrasG12D;Lkb1 mice treated with Vehicle or with catalytic mTOR inhibitor MLN128 for 8 weeks

status: Public on Feb 06 2018

city: Los Angeles

first: David

last: Shackelford

state: CA

address: 10833 LeConte Avenue

department: Division of Pulmonary and Critical Care Medicine

institute: UCLA - David Geffen School of Medicine

summary:
Lung tumors were induced in Kras LSL-G12D; Lkb1 fl/fl mice by intranasal inhalation of Adenoviral Cre. Four weeks after tumor induction, mice were randomly assigned into two groups and treated daily with either Vehicle or 1mg/kg MLN128 for 8 weeks. At the end of the study, mice were euthanized and tumors were dissected out from lung and snap frozen in liquid nitrogen. Frozen tumors were stored in -80C freezer. Lung squamous cell carcinomas adapted to chronic treatement with MLN128
We used microarrays to examine changes in the gene expression in pathways that allowed MLN128 treated squamous cell carcinomas to continue to proliferate in the presence of MLN128

overall_design: Lung tumors were induced in Kras LSL G12D; Lkb1 fl/fl mice by intranasal administration of Adenoviral Cre. Four weeks after tumor induction, mice were randominzed into two groups and treatment started with either Vehicle or 1mg/kg MLN128. Mice were treated daily for 8 weeks. N = 3 squamous cell carcinomas (biological replicates) from Vehicle group; N = 3 squamous cell carcinomas (biological replicates) from MLN128 group.

first: Milica

last: Momcilovic

middle: B


title: Different expression profiles of lncRNAs, mRNAs and circRNAs in preeclampsia and normal placenta (ceRNA)

first: Zhenyu

last: Zhang

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

summary: Preeclampsia is usually considered as a placental basis of diseases, as there are many differently expressed proteins or pathogenic proteins expressed in the placenta. Owing to the important role of post-transcriptional gene regulation in phenotypes and functions of cells, non-coding ribonucleic acid (ncRNA) molecules contributed to the regulation. We collected 7 placental samples from 3 preeclampsia patients and 4 normal women, focused on the basal plate of placenta, as it is the direct connection of mother and fetal, and adopted SBC human ceRNA array V1.0（4×180K）and human miRNA microarray (8*60 K). The results revealed that expressions of 2840 lncRNAs, 1093 mRNAs, 4282 circRNAs and 4 miRNAs were different between preeclampsia and normal placentas. The functions of differentially expressed lncRNAs and co-expressed potential targeting genes were predicted by analyzing Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) biological pathway analysis. Furthermore, we analyzed and find the co-expression and interaction patterns of different RNAs and possible ceRNA mechanism. The present study provided a systematic perspective on the potential function of non-coding RNAs (ncRNAs) in the pathogenesis of preeclampsia.

overall_design: 7 placental samples from 3 preeclampsia patients and 4 normal women were enrolled in. there were no replicates, control and/or reference Samples or dye-swaps.

first: Qiushi

last: Wang

first: Chongdong

last: Liu


title: Expression data from cells located at the invasive front and in the tumor mass of mouse cervical squamous cell carcinomas

status: Public on Feb 01 2018

city: Tokyo

first: Akiko

last: Kunita

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

department: Pathology

institute: University of Tokyo

summary:
Cells located at the invasive front and in the tumor mass of mouse cervical squamous cell carcinomas were isolated by laser microdissection from hematoxylin-stained HPV/E2 sections. 7 months old HPV/E2 mice treated with oestrogen develop invasive cervical squamous cell carcinomas. This model recapitulates human invasive cervical neoplasias.
We used microarrays to compare the transcriptome of cells located at the invasive front versus cells located in the tumor mass of mouse squamous cell carcinomas.

overall_design: 6 samples per condition (invasive front/tumor mass) were captured from one mouse in different parts of the cervical squamous neoplasias.

first: Erik

last: Cabuy

first: Vanessa

last: Baeriswyl


title: TRAF6 Mediates Basal Activation of NF-κB Necessary for Hematopoietic Stem Cell Homeostasis.

status: Public on Jan 31 2018

city: Columbia

first: Jing

last: Fang

state: SC

address: 715 Sumter Street

department: Drug Discovery and Biomedical Sciences

institute: University of South Carolina

summary: The nuclear factor-kB (NF-kB) family of transcription factors is important for hematopoietic function, including development, maintenance, and differentiation of different hematopoietic lineages in response to cytokines and infection. Although ligand-independent or basal NF-kB signaling is required for HSC homeostasis in the absence of inflammation, the upstream tonic mediators of NF-kB signaling are not known. Herein we describe TNF receptor associated factor 6 (TRAF6) as an essential regulator of HSC homeostasis by preserving self-renewal and quiescence through basal activation of NF-kB. Hematopoietic-specific deletion of Traf6 resulted in impaired HSC self-renewal and fitness. Gene expression, RNA splicing, and molecular analyses of Traf6-deficient HSPC revealed changes in adaptive immune signaling, innate immune signaling, and NF-kB signaling, indicating that signaling via TRAF6 in the absence of cytokine stimulation and/or infection occurs in HSPC and is required for HSC function. In addition, we established that loss of NF-kB signaling is responsible for the major hematopoietic defects observed in Traf6-deficient HSPC as deletion of IKKb similarly resulted in impaired HSC self-renewal and fitness. Taken together, our observations position TRAF6 as an essential regulator of HSC homeostasis by maintaining a minimal threshold level of IKKb/NF-kB signaling.

overall_design:
Hematopoietic stem and progenitor cell (HSPC)-enriched lineage-Sca1+Kit+ (LSK) cells were sorted from mice reconstituted with Vav-Cre+ and Traf6-/-;Vav-Cre+ bone marrow cells. Total RNA was extracted from LSK cells and purified with Quick-RNA MiniPrep Kit (Zymogen). RNA quality was determined using the Agilent Bioanalyzer 2100 (Hewelett Packard). 100 ng total RNA was used for enrichment of poly A RNA with the Apollo 324 (WaferGen, Fremont, CA). Poly A RNA was further fragmented (RNase III), adaptor-ligated, and reverse transcribed (Superscript III reverse transcriptase, Lifetech, Grand Island, NY), followed by purification using Agencourt AMPure XP beads (Beckman Coulter, Indianapolis IN). To prepare libraries, universal and index-specific primers, and sample-specific index were added to each adaptor-ligated cDNA sample to amplify the library, followed by purification using AMPure XP beads. The quality and yield of the libraries were assessed on the Bioanalyzer (Agilent, Santa Clara, CA). Libraries at the final concentration of 15 pM were clustered onto a PE flow cell using Illumina's TruSeq PE Cluster kit v3, and sequenced using TruSeq SBS kit on the Illumina HiSeq system.
To study differential gene expression, individually indexed libraries were proportionally pooled (20-50 million reads per sample in general) for clustering in cBot system (Illumina, San Diego, CA). Libraries at the final concentration of 15 pM were clustered onto a single read (SR) flow cell using Illumina’s TruSeq SR Cluster kit v3, and sequenced for 50 bp using TruSeq SBS kit on Illumina HiSeq system.

first: Tomoya

last: Muto

last: Kleppe

first: Lyndsey

middle: C

last: Bolanos

first: Kathleen

last: Hueneman

first: Callum

last: Walker

first: Leesa

last: Sampson

first: Ashley

last: Wellendorf

first: Kashish

last: Chetal

first: Kwangmin

last: Choi

first: Nathan

last: Salomonis

first: Yongwon

first: Yi

last: Zheng

first: Jose

last: Cancelas

first: Ross

last: Levine

first: Daniel

middle: T

last: Starczynowski


title: The colonic epithelium plays an active role in promoting colitis by shaping the tissue cytokine profile

status: Public on Feb 05 2018

city: CAMBRIDGE

first: Jesse

last: Lyons

state: Ma

address: 77 Massachusetts Ave 16-343

department: Bioengineering

institute: Massachusetts Institute of Technology

summary:
BACKGROUND & AIMS: Inflammatory Bowel Disease (IBD) is a chronic inflammatory condition driven by loss of homeostasis between the mucosal immune system, the commensal gut microbiota, and the intestinal epithelium. Our overarching goal is to understand how these components of the intestinal ecosystem cooperate to control homeostasis and to identify novel signal transduction pathways that become dysregulated in IBD. METHODS: We have applied a multi-scale systems biology approach to a mouse model of chronic colitis. We combined quantitative measures of epithelial hyperplasia and immune infiltration with multivariate analysis of inter- and intra-cellular signaling molecules in order to generate a tissue level model of the inflamed disease state. We utilized the computational model to identify signaling pathways that were dysregulated in the context of colitis and then validated model predictions by measuring the effect of small molecule pathway inhibitors on colitis. RESULTS: Our data-driven computational model identified mTOR signaling as a potential driver of inflammation and mTOR inhibition reversed the molecular, immunological, and epithelial manifestations of colitis. Inhibition of Notch signaling, which induces epithelial differentiation, had the same effect, suggesting that the epithelial proliferation/differentiation state plays a key role in maintaining homeostasis of the colon. Confirming this, we found that colonic organoids grown ex vivo showed a similar relationship between proliferation and cytokine expression, even in the absence of gut bacteria and immune cells. CONCLUSIONS: Our study provides a tissue-level systems biology perspective of murine colitis and suggests that mTOR plays a key role in regulating colonic homeostasis by controlling epithelial proliferation/differentiation state.
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 randomly after the onset of inflammation and RNA was isolated from colon tissue from the rectum to proximal-distal junction. This experiment contains expression profiles for 4 Treg-injected negative control animals, 3 severely inflamed animals and 3 moderately inflamed animals.

first: Kevin

last: Haigis

first: Douglas

last: Lauffenburger

first: Alessio

last: Tovaglieri

first: Jessica

last: Gierut

first: Casie

last: Genetti

first: Vijay

last: Yajnik

first: David

last: Breault

first: Phaedra

last: Ghazi

first: Alina

last: Starchenko

first: Emily

last: Poulin

first: Katharine

last: Baldwin


title: Expression data from bone marrow derived macrophages (BMDMs) in Wild Type and NICcA

city: Xi’an

first: Junlong

last: Zhao

state: Shaanxi

address: Chang-Le Xi Street #17

department: Department of Medical Genetics and Developmental Biology

institute: Fourth Military Medical University

summary: The Notch pathway plays a critical role in regulating the development and polarization of macrophages during tumor progression. Therefore, we used BMDMs isolated and cultured from control mice and NICcA mice to compare the gene expression profiles.

overall_design:
BM cells harvested from Ctrl or NICcA mice were stimulated with 25 ng/ml M-CSF (SinoBio) for 7 days to obtain BMDMs. RNA samples of above cells were extracted and sequencing was performed at RiboBio Co., Ltd (Guangzhou, China) with the Illumina HiSeq 3000.

Please note that the mRNA_PROCESSED_DATA.txt file contains both the sequence reads count and processed RPKM (Reads Per Kilobase per Million) data, while the N2_N3--W1_W2_W3.all.transcript.txt file only contains the processed RPKM data.

first: Jun-Long


title: Insulin resistance in 3T3-L1 adipose cells

first: Rima

last: Chaudhuri

summary: 3T3-L1 adipose cells were grown, differentiated and insulin resistance was stimulated by addition of TNF or treatment inlcuding chronic insulin and dexamethasone.

overall_design: Comparison of gene expression in 3T3-L1 cells during treatment with TNF, chronic insuline and dexamethosone; 2-3 samples per group serve as experimental replicates.

first: Zora

last: Modrusan

last: James


title: Role of skeletal muscle in palate development.

status: Public on Jan 30 2018

city: Halifax

first: Boris

last: Kablar

state: Nova Scotia

address: 5850 College Street

department: Medical Neuroscience

institute: Dalhousie University

summary:
The involvement of skeletal muscle in the process of palatal development in mammals is an example of Waddingtonian epigenetics. Our earlier study showed that the cleft palate develops in the complete absence of skeletal musculature during embryonic development in mice. This contrasts with previous beliefs that tongue obstruction prevents the elevation and fusion of the palatal shelves. We argue that the complete absence of mechanical stimuli from the adjacent muscle, i.e., the lack of both static and dynamic loading, results in disordered palatogenesis. We further suggest that proper fusion of the palatal shelves depends not only on mechanical but also on paracrine contributions from the muscle. The muscle's paracrine role in the process of palatal fusion is achieved through its being a source of certain secreted and/or circulatory proteins.
A cDNA microarray analysis revealed differentially expressed genes in the cleft palate of amyogenic mouse fetuses and suggested candidate molecules with a novel function in palatogenesis (e.g., Tgfbr2, Bmp7, Trim71, E2f5, Ddx5, Gfap, Sema3f). In particular, we report on Gdf11 mutant mouse that has cleft palate, and on several genes whose distribution is normally restricted to the muscle (completely absent in our amyogenic mouse model), but which are found down-regulated in amyogenic mouse cleft palate. These molecules probably present a subset of paracrine cues that influence palatogenesis from the adjacent muscle. Future studies will elucidate the role of these genes in muscle-palate crosstalk, connecting the cues produced by the muscle with the cartilage and bone tissue's responses to these cues, through various degrees of cell proliferation, death, differentiation and tissue fusion.

overall_design: Mouse embryos were obtained at E18.5 for RNA extraction and hybridization on Affymetrix microarrays.

first: Irene

last: Rot


title: Role of skeletal muscle in motor neuron development.

summary:
This study describes a cDNA microarray analysis that compared developing mouse MyoD-/- limb musculature (MyoD-dependent, innervated by Lateral Motor Column motor neurons) and Myf5-/- back (epaxial) musculature (Myf5-dependent, innervated by Medial Motor Column motor neurons) to the control and to each other, at embryonic day 13.5 which coincides with the robust programmed cell death of motor neurons and the inability of myogenesis to undergo its normal progression in the absence of Myf5 and MyoD that at this embryonic day cannot substitute for each other.
We wanted to see if/how the myogenic program couples with the neurotrophic one, and also to separate Lateral from Medial column trophic requirements, potentially relevant to Motor Neuron Diseases with the predilection for the Lateral column. Several follow-up steps revealed that Kif5c, Stxbp1 and Polb, differentially expressed in the MyoD-/- limb muscle, and Ppargc1a, Glrb and Hoxd10, differentially expressed in the Myf5-/- back muscle, are actually regulators of motor neuron numbers. We propose a series of follow-up experiments and various ways to consider our current data.

overall_design: Mouse embryos were obtained at E13.5 for RNA extraction and hybridization on Affymetrix microarrays.

first: Mark

last: Baguma-Nibasheka

first: Anna

last: Fracassi

first: Willard

last: Costain

first: Sandra

last: Moreno


title: Insulin resistance in high fat diet mouse (adipose)

summary: Recent discovery reveals HFD insult can cause insulin resistance very rapidly, but the underlying mechanism is still not well understood.We performed a short term experiment in a Diet Induced Insulin resistance mouse model.

overall_design: Comparison of gene expression in adipose tissue during HFD time course (day 5, day 14). Chow diet will serve as control for HFD. 4 samples per group serve as experimental replicates.


title: Expression of genes in the aortic wall of ApoE–/– and ApoE–/–CKIP-1–/– mice

status: Public on Jan 27 2018

city: Beijing

first: Jiao

last: Fan

address: Fuxing road

institute: 301 hospital

summary: The fold-changes for each gene of ApoE–/– CKIP-1–/– with respect to ApoE–/– mice on a 12-week Western diet  were assessed by using three independent Capital Bio mRNA Array.

overall_design: Capital Bio Mouse Genome Oligo Array from Capital Corporation was used for the examination of the expression pattern of genes involved in atherosclerosis. By using different arrays, the fold-change for aortic gene of ApoE–/–CKIP-1–/– mice with respect to ApoE–/– mice on a 12-week Western diet was calculated.

first: Lingqiang

last: Zhang


title: Expression data from macrophages of E-selectin+/+ and E-selectin-/- mouse infected with Listeria monocytogenes in vivo on day3

status: Public on Jan 25 2018

first: xiaoqing

last: xu

address: No.5 Dongdan Santiao, Dongcheng District

department: Immunology

institute: Chinese Academy of Medical Sciences

summary: We used microarrays to detail the global gene expression in peritoneal macrophages (PM) from  E-selectin+/+ and E-selectin-/- mouse infected with Listeria Monocytogenes in vivo on day3

overall_design: Peritoneal macrophages collected from  E-selectin+/+ and E-selectin-/- mouse infected with Listeria Monocytogenes in vivo on day3   were for RNA extraction and hybridization on Affymetrix microarrays.

first: Xiaoqing

last: Xu

first: Xujia

last: Xue

first: Tao

last: Cao


title: A non-lymphoid origin for lymph node resident memory T cells

city: Minneapolis

first: Marissa

last: Macchietto

state: MN

department: Institute of Health Informatics

institute: University of Minnesota

summary: Immunosurveillance of secondary lymphoid organs (SLO) is performed by central memory T cells that recirculate through blood. Resident memory T cells (TRM) remain parked in nonlymphoid tissues and often stably express CD69. We recently identified TRM within SLO, and this study addresses knowledge gaps in their origin and phenotype. Parabiosis of ‘dirty’ mice revealed that CD69 expression is insufficient to infer stable residence. Using selective depletion strategies, parabiosis, imaging, tissue grafting, and photoactivatable T cells, we report that restimulation of TRM within the skin or mucosa results in a substantial increase in TRM that patrol all regions of draining lymph nodes. SLO TRM were derived from nonlymphoid tissue residents. Transcriptional profiling and flow cytometry revealed a refined phenotype shared between both nonlymphoid and SLO TRM. These data demonstrate the nonlymphoid origin of SLO TRM and suggest vaccination strategies by which memory CD8 T cell immunosurveillance can be regionalized to specific lymph nodes.

overall_design: A total of 3 cell populations were analyzed, with 3 replicates per population. Total RNA was isolated from FACS-sorted memory CD8+ memory P14 T cells >30 days after LCMV armstrong infection. Sorted populations include splenic CD62Lhi CD69lo TCM cells, splenic CD62Llo CD69hi TRM cells, and CD62Llo CD69hi CD103lo FRT TRM cells.

first: Lalit

middle: K

last: Beura

first: Sathi

last: Wijeyesinghe

first: Emily

last: Thompson

first: Pamela

last: Rosato

last: Pierson

first: Jason

last: Schenkel

first: Vaiva

last: Vezys

first: Brian

last: Fife

first: Steven

last: Shen

first: David

last: Masopust


title: Microarray data of benzo[a]pyrene-treated WHCO1 vs EPC-2 cells

status: Public on Jan 18 2018

city: Cape Town

first: Alexis

last: Bick

state: Western Cape

address: Anzio Road, Observatory

department: Division of Medical Biochemistry and Structural Biology

country: South Africa

institute: University of Cape Town

summary: The aim of this project was to investigate the differential effects of benzo[a]pyrene (BaP) treatment on global gene transcription, comparing normal (EPC-2) and cancer (WHCO1) cell lines from the oesophagus, in order to further our understanding of the molecular mechanisms of BaP-induced development and maintenance of oesophageal squamous cell carcinoma.

overall_design: Two cell lines (WHCO1, esophageal squamous cell carcinoma and EPC2-hTERT, telomerase-immortalized normal esophageal cell line) were used. For both cell lines total RNA was extracted from a vehicle control (Untreated) and treatment with 10 uM benzo[a]pyrene after 24 hours treatment, with biological repeat duplicate samples for each treatment. 8 samples in total


title: Expression data from livers of ad libitum and calorie-restricted mice

first: De-Pei

last: Liu

address: Dong Dan San Tiao 5, Dongcheng District

institute: Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences

summary:
Caloric restriction (CR) slows the ageing process in many orgamisms, including mice. Liver is an important metabolic organ with active RNA expression. CR reprogrammes hepatic metabolism as well as hepatic transcriptome.
We sought to study CR-induced transcriptomic changes in mouse liver to investigate the anti-ageing mechanisms of CR.

overall_design: Eight-week-old male WT C57BL/6J mice were housed individually and were randomly allocated into 2 groups (3 mice per group). AL mice were fed AL food ad libitum for 12 weeks. CR mice were fed a 20% restricted diet for the first week and a 40% restricted diet for the remaining 11 weeks of the CR diet. Then the livers were collected and the hepatic RNAs were extracted for microarray analysis.

first: Ran

last: Zhang


title: Endothelial gene expression analysis after silencing the lncRNA GATA6-AS using LNA GapmeRs.

status: Public on Jan 24 2018

city: Frankfurt am Main

first: Philipp

last: Neumann

address: Theodor-Stern-Kai 7

institute: Institute for Cardiovascular Regeneration

summary:
Impaired or excessive growth of endothelial cells contributes to several diseases. However, the functional involvement of regulatory long non-coding RNAs in these processes is not well defined. Here we show that the long non-coding antisense transcript of GATA6 (GATA6-AS) interacts with the epigenetic regulator LOXL2 to regulates endothelial gene expression via changes in histone methylation. Using RNA deep sequencing, we find that GATA6-AS is up-regulated in endothelial cells during hypoxia. Silencing of GATA6-AS diminishes TGF-β2-induced endothelial-mesenchymal transition in vitro and promotes formation of blood vessels in mice. We identify LOXL2, known to remove activating H3K4me3 chromatin marks, as a GATA6-AS-associated protein, and reveal a set of angiogenesis-related genes that are inversely regulated by LOXL2 and GATA6-AS silencing. As GATA6-AS silencing reduces H3K4me3 methylation of two of these genes, periostin and cyclooxygenase-2, we conclude that GATA6-AS acts as negative regulator of nuclear LOXL2 function.
In this dataset we include the global gene expression analysis using exon arrays after silencing the lncRNA GATA6-AS.

overall_design: 4 samples were analyzed. Data was uploaded to and analyzed by the noncoder web interface with default parameters. Mean values of LNA Ctl and LNA GATA6-AS replicates were build and used for fold change LNA GATA6-AS vs. LNA Ctl calculation.

first: Nicolas

last: Jaé


title: Defective XRN3-mediated transcription termination in Arabidopsis affects the expression of protein-coding genes [array]

city: Warsaw

first: Michal

last: Krzyszton

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics, Polish Academy of Sciences

summary: Arabidopsis thaliana contains two nuclear XRN2/3 5'-3' exonucleases that are homologs of yeast and human Rat1/Xrn2 proteins involved in the processing and degradation of several classes of nuclear RNAs and in transcription termination of RNA polymerase II. Using strand-specific short read sequencing we show that knockdown of XRN3 leads to an altered expression of hundreds of genes and the accumulation of uncapped and polyadenylated read-through transcripts generated by inefficiently terminated Pol II. Our data support the notion that XRN3-mediated changes in the expression of a subset of genes are caused by upstream read-through transcription and these effects are enhanced by RNA-mRNA chimeras generated in xrn3 plants. In turn, read-through transcripts that are antisense to downstream genes may trigger production of siRNA. Our results highlight the importance of XRN3 exoribonuclease in Pol II transcription termination in plants and show that disturbance in this process may significantly alter gene expression.

overall_design: Col-0 and xrn3-8 before and after cordycepin treatment inhibiting transcription. Each genotype and condition in three biological replicas.

first: Monika

last: Zakrzewska-Placzek

first: Aleksandra

last: Kwasnik

first: Norbert

last: Dojer

first: Wojciech

last: Karlowski

first: Joanna

last: Kufel


title: RNA bisulfite sequencing of candidate tRNAs in Drosophila melanogaster

status: Public on Jan 16 2018

city: Vienna

first: Schaefer

last: Matthias

state: AT

address: Schwarzspanierstrasse 17-I

department: Cell and Developmental Biology

country: Austria

institute: Medical University Vienna, Center for Anatomy & Cell Biology

type: Methylation profiling by high throughput sequencing

summary: Dnmt2 and NSun2 are (cytosine-5) RNA methyltransferases. Using CRISPR/Cas9 we created null mutations in Dnmt2 and NSun2 genes in Drosophila melanogaster. We also ectopically expressed a wild type and catalytically inactive Dnmt2 form in the Dnmt2 mutant background. RNA bisulfite sequencing was used to follow RNA methylation at partical tRNA substrates.

overall_design: Measuring (cytosine-5) RNA methylation levels in various tRNAs from adult wild type controls, Dnmt2 and NSun2 mutants, and ectopically expressed Dnmt2 in the Dnmt2 null mutant background.

first: Bianca

last: Genenncher

first: Matthias

last: Schaefer


title: Transcriptome profiles of mouse embryonic stem cells cultured in different conditions by RNA-seq analysis

status: Public on Jan 20 2018

city: Tianjin

first: Renpeng

last: Guo

address: Weijin Road 94th, Nankai District, Tianjin, China

institute: Nankai University

summary: Pluripotent mouse embryonic stem cells (ESCs) were originally derived and stably maintained on feeder cells such as inactivated mouse embryo fibroblasts, and can generate complete ESC-pups by tetraploid embryo complementation (TEC), the most stringent functional test of naive pluripotency. Remarkably, 2i (inhibitors of Mek and Gsk3β signaling) medium with LIF in the absence of serum and feeders was developed to achieve ground state of mouse ESCs, and also has been successfully used for derivation of germline competent ESCs in other species such as rat. Notably, 2i-culture gives rise to transcriptional profiles and epigenetic landscapes quite distinct from serum-based ESCs. To better understand transcriptional landscape and signal transductions, we performed RNA-seq analysis of ESCs cultured in four different conditions: serum without feeder, serum with feeder, serum with feeder and 2i, and N2B27+2i.

overall_design: We sought to investigate the differentiated expressed genes of N33 ESCs cultured in four conditions: serum without feeder (on gelatin, N33_G), serum with feeder (N33_F), serum with feeder and 2i (N33_F2i), and N2B27+2i (N33_NB2i). ESCs with biological duplicates were collected for RNA extraction and RNA-seq analysis simultaneously.

first: Lin


title: Expression data from breast cancer tissues and adjacent normal tissues

status: Public on Jan 13 2018

city: Taipei

first: Jer-Wei

last: Chang

address: 5F-13, No.27, Sec.2, Fuxing S. Rd.,

country: Taiwan

institute: Mao Ying Genetech Inc.

summary: The early-onset breast cancer patients (age ≤40) often display higher incidence of axillary lymph node metastasis, and poorer five-year survival than the late-onset patients. To identify the genes and molecules associated with poor prognosis of early-onset breast cancer, we examined gene expression profiles from paired breast normal/ tumor tissues, and coupled with Gene Ontology and public data base analysis. Our data showed that the expression of GAS7b gene was lower in the early-onset breast cancer patients as compared to the elder patients. We found that GAS7 was associated with CYFIP1 and WAVE2 complex to suppress breast cancer metastasis via blocking CYFIP1 and Rac1 protein interaction, actin polymerization, and β1-integrin/FAK/Src signaling. We further demonstrated that p53 directly regulated GAS7 gene expression, which was inversely correlated with p53 mutations in breast cancer specimens. Our study uncover a novel regulatory mechanism of p53 in early-onset breast cancer progression through GAS7-CYFIP1 mediated signaling pathways.

overall_design: The total RNA of 25 sets of normal/ tumor pair of breast tissue specimens was extracted, and analyzed by Affymetrix Human Exon 1.0 ST Array.

first: Jer

first: Wen

middle: H

last: Kuo

first: Chiao

last: Lin

first: Shih

last: Chan

first: Yih

last: Uen

first: Lu

last: Wang


title: Endothelial gene expression analysis after silencing LOXL2 using siRNAs

first: Philipp

last: Neumann

summary:
Impaired or excessive growth of endothelial cells contributes to several diseases. However, the functional involvement of regulatory long non-coding RNAs in these processes is not well defined. Here we show that the long non-coding antisense transcript of GATA6 (GATA6-AS) interacts with the epigenetic regulator LOXL2 to regulates endothelial gene expression via changes in histone methylation. Using RNA deep sequencing, we find that GATA6-AS is up-regulated in endothelial cells during hypoxia. Silencing of GATA6-AS diminishes TGF-β2-induced endothelial-mesenchymal transition in vitro and promotes formation of blood vessels in mice. We identify LOXL2, known to remove activating H3K4me3 chromatin marks, as a GATA6-AS-associated protein, and reveal a set of angiogenesis-related genes that are inversely regulated by LOXL2 and GATA6-AS silencing. As GATA6-AS silencing reduces H3K4me3 methylation of two of these genes, periostin and cyclooxygenase-2, we conclude that GATA6-AS acts as negative regulator of nuclear LOXL2 function.
In this dataset we include the global gene expression analysis using exon arrays after silencing LOXL2.

overall_design: 7 samples were analyzed. Data was uploaded to and analyzed by the noncoder web interface with default parameters. Mean values of siCtl and siLOXL2 replicates were build and used for fold change siLOXL2 vs. siCtl calculation.

first: Nicolas

last: Jaé


title: PBMC gene expression from Crohn's disease patients before Infliximab therapy.

city: Haifa

first: Shai

last: Shen-Orr

address: 1st Efron Street

country: Israel

institute: Rappaport Institute of Medical Research, Faculty of Medicine and Faculty of Biology, Technion

summary: About 40% IBD patients treated with anti-TNF antibodies do not respond to therapy. Baseline biomarkers of response are therefore of interest. By combining computational deconvolution of gene expression and meta-analysis approaches we identified cellular biomarkers in tissue (validated in 2 cohorts by IHC of biopsies), and investigated associated gene biomarkers in blood. This dataset provides data from the validation cohort III (blood).

overall_design: Whole blood samples were collected from 22 patients diagnosed with Crohn's disease, just before starting anti-TNF therapy (Infliximab). All patients were naive to anti-TNF. Response to therapy was assessed after 14 weeks based on changes in CRP and Calprotectin, as well as endoscopy (Responders: 17; Non-responders: 5). The prognostic power of genes identified to be related to cellular biomarkers identified from meta-analysis of public datasets of biopsy tissues were investigated.

first: Renaud

last: Gaujoux

first: Elina

last: Starosvetsky

first: Naama

last: Maimon

first: Francesco

last: Vallania

first: Yehuda

last: Chowers

first: Purvesh

last: Khatri


title: HIV-1 indcued genes in human monocyte-derived macrophages

status: Public on Jan 09 2018

city: Gainesville

first: Mark

last: Wallet

state: Florida

address: 1275 Center Drive

institute: University of Florida

summary: HIV-1 infection of monocyte-derived macrophages does not elicit a detectable type I IFN response in vitro, however, previously published data has shown that blocking STAT1 and STAT3 inhibits HIV-1 replication. Here we test to see if low levels of IFN inducible genes are detectable in human monocyte-derived macrophages that have been infected with HIV-1 in vitro.

overall_design: Monocytes from 5 healthy human donors were differentiated into macrophages in vitro and infected with HIV-1-AD for 7 days. Total RNA was isolated and gene expression was assessed.

first: Jared

middle: P

last: Taylor

first: Melanie

middle: N

last: Cash

first: Katherine

middle: E

last: Santostefano

first: Mahito

last: Nakanishi

first: Naohiro

last: Terada


title: Expression data for Tcl1 tg mice compared to CD44ΔB Tcl1 tg mice

city: Salzburg

first: Julia

middle: Christine

last: Gutjahr

address: Müllner Hauptstraße 48

department: Department of Internal Medicine III, Paracelsus Medical University

institute: SCRI-LIMCR

summary:
Tcl1 tg mice develop a chronic lymphocytic leukemia (CLL) -like disease. To investigate the contribution of the adhesion molecule CD44 to CLL pathophysiology, we developed a CD19Cre CD44flox/flox Tcl1 tg mouse with a B cell specific CD44 deficiency (CD44ΔB Tcl1 tg).
We used the Clariom S mouse microarray from Affymetrix to investigate transcriptional differeneces between Tcl1 tg and CD44ΔB Tcl1 tg mice

overall_design: CD5+/CD19+ malignant B cells isolated from splenocytes from 4 different Tcl1 tg mice and 4 different CD44ΔB Tcl1 tg were used for RNA extraction and hybridization on Affymetrix microarrays.

first: Tanja

last: Hartmann


title: Expression data from mouse basal cell carcinoma (BCC) and normal epidermis, and BCC cell line treated with cyclopamine

status: Public on Jan 15 2018

city: Sendai

first: yuriko

last: saiki

state: Miyagi

address: 2-1 Seiryo-machi, Aoba-ku

department: Molecular Pathology

institute: Tohoku University School of Medicine

summary:
Activation of the Sonic hedgehog (Shh) signaling pathway due to Patched 1 (PTCH1) mutation is a key event in sporadic and familial basal cell carcinoma (BCC) development.  To find out the specific pathway for therapeutic intervention, we developed a mouse BCC model by skin specific Ptch1 inactivation, and sought to identify novel Shh targets.

We used microarrays to identify up-regulated genes in mouse BCC.

We used microarrays to identify down-regulated genes in mouse BCC cell line by cyclopamine.

overall_design:
Basal cell carcinoma and epidermis were dissected for RNA extraction and hybridization on Affymetrix microarrays.

Basal cell carcinoma cell line was incubated with cyclopamine, and subjected to RNA extraction and hybridization on Affymetrix microarrays.

first: Yuriko

last: Saiki

first: Tetsuo

last: Noda


title: ID4 function antagonizes OLIG1 and OLIG2 to suppressive aggressive glioma

status: Public on Jan 02 2018

city: Boston

first: Alvin

middle: T.

last: Kho

state: MA

address: 320 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

summary: The basic helix-loop-helix proteins Olig1 and Olig2 are expressed in high grade, aggressive human glioblastoma multiformes (GBMs). Here we investigated genetic mechanisms regulating Olig1/2 function during gliomagenesis. Although Olig2 function is necessary for early-aggressive tumor formation in a genetically relevant model of classic GBMs with intact p53 function, late-onset gliomas do eventually form. Using an unbiased approach, we identified Id4, encoding a negative HLH protein, as a gene target potently repressed by Olig2 in glioma progenitors. Although Id4 is thought to antagonize proneural genes involved in differentiation, we report a paradoxical role for Id4 in glioma. Genetic deletion of Id4 converts Olig2-/- gliomas to the early-aggressive form, and conversely, overexpression of Id4 inhibits intact Olig2 and prevents even late-onset tumors. Olig1 overexpression is sufficient for gliomagenesis in an Id4-dependent manner.  Together, these findings indicate that gliomagenic factors Olig1 and Olig2 are opposed by Id4 function, which acts as tumor suppressor in p53-intact gliomas.

overall_design:
Analysis of the transcriptomes of Olig vs. Olig-deficient gliomagenic progenitor cells.
11 distinct conditions with biological replicates: Olig1/2-/-  Ink4a/Arf-/- EGFRvIII cells (n=6), Olig1/2+/- Ink4a/Arf-/- EGFRvIII cells (n=3), Olig1/2+/+ Ink4a/Arf-/- EGFRvIII cells (n=3), Olig1/2-/- Ink4a/Arf-/- EGFRvIII cells overexpressing GFP (n=3), Olig1/2+/- Ink4a/Arf-/- EGFRvIII cells overexpressing GFP (n=2), Olig1/2-/- Ink4a/Arf-/- EGFRvIII cells overexpressing Olig2 (n=3), Olig1/2+/- Ink4a/Arf-/-EGFRvIII cells overexpressing Olig2 (n=2), Olig1/2-/- forebrain E18.5 (n=2), Olig1/2+/- forebrain E18.5 (n=2), Olig1/2-/- spinal cord E18.5 (n=2) and Olig1/2+/- spinal cord E18.5 (n=2).

first: Emmanuelle

last: Huillard

first: Keith

last: Ligon

first: David

last: Rowitch


title: Transcriptomic dissection of Bradyrhizobium sp. strain ORS285 in symbiosis with Aeschynomene spp. inducing different bacteroid morphotypes with contrasted symbiotic efficiency

status: Public on Jan 05 2018

city: Gif sur Yvette

first: Florian

last: Lamouche

address: 1, Avenue de la Terrasse

department: Institute of Integrative Biology of the Cell (I2BC)

country: France

institute: Centre national de la Recherche Scientifique (CNRS)

summary: To circumvent the paucity of nitrogen sources in the soil Legume plants evolved a symbiotic interaction with nitrogen-fixing soil bacteria called rhizobia. During symbiosis, legumes form root organs called nodules, where bacteria are housed intracellularly and become active nitrogen fixers known as bacteroids. Depending on their host plant, bacteroids can adopt different morphotypes, being either unmodified (U), elongated (E) or spherical (S). E- and S-typr bacteroids undergo a terminal differentiation leading to irreversible morphological changes and DNA endoreduplication. Previous studies suggest that differentiated bacteroids display an increased symbiotic efficiency (E>U & S>U). In this study, we used a combination of Aeschynomene species inducing E- and S-type bacteroids in symbiosis with Bradyrhizobium sp. ORS285 to show that S- performed better than E-type bacteroids. Thus, we performed a transcriptomic analysis on E- and S-type bacteroids to identify the bacterial functions involved in each bacteroid type.

overall_design: 3 conditions with 3 replicates each for each condition are analyzed. Two bacteroid conditions are compared : S-type bacteroids from A. indica nodules and E-type bacteroids from A. afraspera nodules, as well as a culture reference in rich medium

first: Djamel

last: Gully

first: Anaïs

last: Chaumeret

first: Camille

last: Verly

first: Olivier

last: Pierre

first: Coline

last: Sciallano

first: Joël

last: Fardoux

first: Christian

last: Jeudy

first: Attila

last: Szücs

first: Samuel

last: Mondy

first: Yves

last: Dessaux

first: Christophe

last: Salon

last: Kereszt

first: Eric

last: Giraud

first: Peter

last: Mergaert

first: Benoit

last: Alunni


title: Peroxisomal membrane channel Pxmp2 is essential for development of mammary gland epithelium in mice

status: Public on Dec 31 2017

city: Oulu

first: Vasily

middle: D.

last: Antonenkov

address: Kottinkangas

department: Faculty of Biochemistry and Molecular Medicine

country: Finland

institute: University of Oulu

summary: To understand the functional role of peroxisomal membrane channel Pxmp2, mice with a targeted disruption of the Pxmp2 gene were developed. These mice were viable, grew and bred normally. However, Pxmp2-/- were unable to nurse their pups due to retarded mammary ductal outgrowth associated with reduced proliferation of epithelial cells during puberty. Transplantation experiments established the Pxmp2-/- mammary stroma as a tissue responsible for suppression of epithelial growth. Morphological and biochemical examination revealed the presence of peroxisomes in mammary adipocytes, and functional Pxmp2 was detected in the stroma of WT mice. Comparative microarray analysis of WT and Pxmp2-/- mammary fat pad identified an expanded set of differentially expressed genes involved in the regulation of epithelial development. The data point to the possible role of lipid-sensing receptors in mechanisms linking Pxmp2 deficiency and suppression of mammary epithelial growth. The hypothesis was verified using the PPARα agonist clofibrate, which was able to avert pubertal development of mammary epithelium in WT mice. However, treatment of Pxmp2-/- mice with PPARα antagonist MK886 could only partially restore epithelial growth suggesting that several lipid-sensing or other receptors may be affected by Pxmp2 deficiency. The data reveal impaired mammary gland development as a new category of peroxisomal disorders.

overall_design: Microarray analysis was used to compare the gene expression profiles of mammary fat pads of Pxmp2-/- and WT mice (three mice per group). All mice were ovariectomized at the age of 21 days and injected with estradiol at the age of 31 days to standardize the time of the initiation of puberty. The mice were sacrified 8 h thereafter and samples were collected for RNA extraction.

first: Miia

last: Vapola

first: Aare

last: Rokka

first: Raija

last: Sormunen

first: Jussi

last: Vuoristo

first: Leena

last: Alhonen

first: Werner

last: Schmitz

first: Ernst

last: Conzelmann

first: Marjut

last: Kreivi

first: Anni

last: Wärri

first: Silke

last: Grunau

middle: D

first: J

last: Hiltunen


title: Cardiac microarray changes in a transgenic mouse expressing a human mitochondrial progesterone receptor (PR-M).

status: Public on Dec 27 2017

city: Durham

first: Thomas

middle: M

last: Price

state: NC

address: 5704 Fayetteville Rd

institute: Duke University

summary:
A TET-On transgenic mouse model was develop for cardiac expression of a human mitochondrial progesterone receptor (PR-M). Expression was verified by immunohistochemistry and RT-PCR. Previous research with cell knockdown and overexpression has shown a ligand dependent increase in cellular respiration with this receptor.
Mice expressing (N=3) or not expressing (N=3) PR-M were treated with progesterone for 19-21 days prior to sacrifice. Tissue from the apical cardiac ventrical was submitted for microarray.

overall_design: Total RNA isolated from the cardiac ventricular apex was used for hyridization on a Affymetrix Mouse Genome 430 2.0 Array.

first: Qunsheng

last: Dai

first: Zhengzheng

last: Wei


title: RNA-seq Facilitates Quantitative Analysis of Wild Type and RXRα-silenced HepG2-NTCP Cell Transcriptomes

status: Public on Dec 21 2017

first: Zhiyi

last: Jing

address: 7 Science Park Road ZGC Life Science Park

institute: NIBS

summary: The goals of this study are to check mRNA levels of genes and pathways regulated by RXRα knocking down, and figure out their influences to HBV infection. The mRNA profiles of wild-type (WT) and RXRα knockdown (RXRα-KD) HepG2-NTCP cells were generated by deep sequencing using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the gene level with TopHat followed by Cufflinks. Using an optimized data analysis workflow, we mapped about 40 million sequence reads per sample to the human genome. We find arachidonic acid synthesis, retinol metabolism pathways and serveral other genes are regulated by RXRα knockdown. We also revealed that reduced gene expression in arachidonic acid (AA)/eicosanoids biosynthesis pathways, in particular one of the AA synthases Phospholipase A2 Group IIA (PLA2G2A), is associated with increased HBV infection. Moreover, we also found exogenous treatment of AA inhibits HBV infection. These data implicate the  participation of AA/eicosanoids biosynthesis pathways in the regulation of HBV infection, and point to a novel potential strategy for host-targeted therapies against HBV.

overall_design: Examination of 2 different mRNA profiles in 2 cell lines. Reference to SRA study SRP121524 and BioProject PRJNA414179.

first: Wenhui

last: Li

first: Mei

last: Song


title: Sorafenib promotes graft-versus-leukemia activity in mice and humans through IL-15 production in FLT3-ITD mutant leukemia cells

status: Public on Dec 19 2017

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

summary: Patients relapsing with FLT3-ITD mutant acute myeloid leukemia (AML) after allogeneic hematopoietic cell transplantation (allo-HCT) have a one-year-survival below 20%. We  observed that sorafenib increased IL-15 production by FLT3-ITD+-leukemia cells, which synergized with the allogeneic CD8+T-cell response, leading to long-term survival in murine   and humanized FLT3-ITD+AML models. Using IL-15 deficiency in recipient tissues or leukemia cells, IL-15 production upon sorafenib-treatment could be attributed to leukemia cells. Sorafenib treatment-related IL-15 production caused an increase in CD8+CD107a+IFN-γ+ T-cells with features of longevity (Bcl-2high/reduced PD-1-levels), which eradicated leukemia in secondary recipients. Mechanistically, sorafenib reduced ATF4 expression, thereby blocking negative regulation of IRF7-activation, which enhances IL-15 transcription. Consistent with the mouse data, IL-15 and pIRF7 levels increased in leukemic blasts of  FLT3-ITD+AML patients upon sorafenib treatment. Analysis of 130 patients with FLT3-ITD-mutant AML relapsing after allo-HCT showed the highest complete remission-rate and median overall-survival-rate in the sorafenib/donor lymphocyte infusion (DLI) group compared to all other groups (chemotherapy, chemotherapy/DLI, sorafenib alone). Our findings indicate that the synergism of DLI and sorafenib is mediated via reduced ATF4 expression, causing activation of the pIRF7/IL-15-axis in leukemia cells. The sorafenib/DLI strategy therefore has the potential for an immune-mediated cure of FLT3-ITD-mutant AML-  relapse, an otherwise fatal complication after allo-HCT.

overall_design: Peripheral blood mononuclear cells (PBMC) from patients relapsing after allograft transplantation were extracted three days before and six days after treatment with sorafenib. 4 patients, marked as responders, showed a favorable outcome event after 6 months, while 4 patients. marked as non-responders. did not respond to sorafenib treatment.

first: Melanie

last: Boerries

first: Robert

last: Zeiser

first: Dietmar

last: Pfeifer

first: Sandra

last: Dunesque


title: Genome-wide analysis of gene expression in VECs and CFs after co-culture

status: Public on Dec 30 2017

city: Xi'an

first: Jinqing

state: Shaanxi Province

address: 569 Xinsi Road

department: Department of Plastic and Burn Surgery

institute: Tangdu Hospital, Fourth Military Medical University

summary: The gene expression in vascular endothelial cells (VECs) and circulating fibrocytes (CFs) was tested either culturing alone or co-cultured. Our previous study showed that CFs inhibit both proliferation and apoptosis of VECs. In this present study, we co-cultured CFs and VECs in Transwell and tested the gene expression in CFs and VECs in order to delight the mechanism under which CFs affect the proliferation and apoptosis of VECs.

overall_design: CFs and VECs were either cultured alone or co-cultured in Transwell with each other for 24 hours. Then total RNA was extracted from CFs cultured alone, CFs co-cultured with VECs, VECs cultured alone and VECs co-cultured with CFs.

first: Xueyong


title: Effect of Serum Response Factor (SRF) gene deletion on the adult cardiac gene expression at baseline and in response to phenylephrine

city: Châtenay-Malabry

first: Mathias

last: Mericskay

address: 5, Rue Jean-Baptiste Clément

department: Signalling and Cardiovascular Pathophysiology

institute: INSERM - University Paris-Sud

summary:
The objective of this study is to assess the effects of the Serum Response Factor deletion on the cardiac gene expression program at different time points after the deletion (day 8 and day 25) and to compare the response of SRF-deficient heart and control heart to phenylephrine, an alpha-adrenergic agonist triggering cardiac hypertrophy.
To generate cardiomyocyte-specific SRF knockout, 10 week-old mice homozygous for the [SRF-flex2neo] allele bearing one copy of the [alphaMHC-MerCreMer] transgene (SRFHKO mice) (Reference 1)  were injected i.p. with 0.7mg of tamoxifen for 3 days. All control (SRF-flex2neo littermates) and SRFHKO mice were systematically injected with tamoxifen to normalize for any effects due to tamoxifen. For the mice treated with phenylephrine (PE), the drug was administrated at 80 mg/kg/day from day 10 to day 25 after the first day of tamoxifen injection, using Alzet osmotic minipumps. Reference: Temporally controlled onset of dilated cardiomyopathy through disruption of the SRF gene in adult heart. Parlakian A, Charvet C, Escoubet B, Mericskay M, Molkentin JD, Gary-Bobo G, De Windt LJ, Ludosky MA, Paulin D, Daegelen D, Tuil D, Li Z. Circulation. 2005 Nov 8;112(19):2930-9. PMID: 16260633

overall_design: Mice were sacrificed 8 days or 25 after tamoxifen injection for RNA extraction and hybridization on Affymetrix microarrays. There are 6 groups of mice. At day 8 , 2 controls and 4 SRFKO mutants were analyzed. At day 25, there are 3 untreated controls, 3 untreated SRFHKO mutants, 3 PE treated controls, 3 PE treated SRFHKO mutants.

first: Zhenlin


title: Plant-derived compounds strigolactone GR24 and pinosylvin modulate gene expression in rat L6 skeletal muscle cells

status: Public on Dec 18 2017

city: Kuopio

first: Tarja

last: Kokkola

address: Yliopistonranta 1 C

department: School of Medicine / Internal Medicine

institute: University of Eastern Finland

summary: We investigated the effects of novel SIRT1 activating plant-derived compounds strigolactone GR24 and pinosylvin on gene expression in rat L6 skeletal muscle myotubes. Resveratrol was included in analyses as a reference compound.

overall_design: Myotubes were treated with 60 micromolar test compounds in DMSO or equivalent concentration of DMSO (control) for 24 h. Three independent experiments were performed from the same batch of cells.

first: Shalem

last: Modi

first: Nagendra

last: Yaluri

first: Markku

last: Laakso


title: Characterization of distinct states of human naïve and primed pluriopotency

status: Public on Dec 13 2017

city: Osaka-Sayama

first: Toshiyuki

last: Takehara

state: Osaka

address: 377-2, Ohno-Higashi

department: Faculty of Medicine

institute: Kindai Universty Hospital

summary:
Pluripotency of mammalian stem cells is stabilized at different status depending upon the extracellular stimuli of their environment. Now, there is a consensus that mouse embryonic stem cells (mESCs) and iPSCs (miPSCs) represent undifferentiated status very close to ground-state of mammalian development when cultured in optimal condition. Since they have not been activated to commit into any lineages, they are stated as “naïve-state stem cells”. In contrast, human ESCs (hESCs), hiPSCs, and mEpiSCs are considered to possess partially differentiated characteristics compared with mESCs and miPSCs. Thus, they are stated as “primed-state stem cells”. Investigation of the prerequisites for establishment of the naïve-state is significantly important to fully understand mammalian development and to extrapolate the technologies developed with mouse ES/iPS cells for human.
We used expression data to understand the gene expression profile and identified distinct characteristics on pluripotent state.

overall_design: Human induced pluripotent stem cell was traditionally maintained in primed-state. And also, we obtained converted naïve state pluripotent stem cell. Characteristics analysis was perfomed to investigate and compare the gene expression profile in each samples.

first: Takeshi

last: Teramura

first: Hirofumi

last: Suemori


title: Molecular and cellular alterations associated with long-term murine mammary cancer prevention following short-term tamoxifen chemoprevention indicate luminal progenitor cells as targets

city: Savannah

first: Amy

last: Greene

state: GA

address: 1250 East 66th Street

department: Biomedical Sciences

institute: Mercer University

summary:
Limited term administration of tamoxifen for 2-8 years results in long-term prevention of estrogen receptor positive (ER+) breast cancer as demonstrated in several clinical trials.  How the memory of tamoxifen is initiated and maintained, as well as which cells are involved and what molecular messages are transmitted, is undefined.  Understanding these features of this robust chemopreventive agent will lead to significant advancement in our knowledge of how a healthy breast environment is supported.  The purpose of this study was to determine the molecular message that reflects a long-term and efficacious memory of tamoxifen.
We used microarrays to identify genes with a significant long-term alteration in expression level following a short-term exposure to tamoxifen as a chemopreventive.

overall_design: A total of 20 samples were analyzed, 10 from tamoxifen treated animals and 10 from placebo treated animals.  One number 4 mammary gland was isolated and used in preparation of the microarray probe 30 days after the completion of treatment.  Animals were monitored for mammary tumor formation up to 2 years of age following collection of the microarray sample gland and tumor outcome was scored.  Statistical comparisons of gene expression were made between animals that presented with tumor formation (10 animals) and those that did not form tumors (10 animals) up to 2 years of age.

first: Teresa

middle: A

last: Rose-Hellekant

middle: L

first: Ronald

middle: R

last: Regal

first: Ming

middle: Q

last: Duan

first: Olga

last: Zhdankin

first: Andrew

last: Skildum

first: Jon

last: Holy

first: Donna

last: Parke

last: Bomier


title: m6A-seq in wild-type and Gsk-3-deficient mouse embryonic stem cells

city: Denver

first: Christopher

last: Phiel

state: CO

address: 1150 12th Street SI 4111

department: Integrative Biology

institute: University of Colorado Denver

summary: Quantification of m6A-modified mRNA in mouse embryonic stem cells - 2 cell types

overall_design: Quantification of m6A-modified mRNA in mouse embryonic stem cells - WT and Gsk-3 DKO

middle: J


title: Expression data from distal ileum of mice administered lactic acid bacteria, Lactococcus lactis C59 and Lactobacillus rhamnosus GG

status: Public on Dec 10 2017

city: Tsukuba

first: Chise

last: Suzuki

state: Ibaraki

address: 2 Ikenodai

department: Animal Products Res. Division

institute: NARO Institute of Livestock and Grassland Science

summary:
This study aimed to investigate the effects of oral administration of lactic acid bacteria (LAB) on gene expression in murine ileum.
To evaluate the strain specific and dose effects of LAB on the gene expression of distal ileum, Lactococcus lactis C59 and Lactobacillus rhamnosus GG were administered at a dose of 1 x 107 cells (10^7), 1 x 108 (10^8) cells or 1 x 109 (10^9) cells
Microarray analysis was performed using total RNA from distal ileum to detail the gene expression of 7 groups; control, C59- and GG-administered at a dose of 1 x 107 cells (10^7), 1 x 108 (10^8) cells or 1 x 109 (10^9) cells.
Gene expression patterns were clustered by administered strains.
Several genes involved in immune system are up-regulated in the lower intestine in the presence of GG and down-regulated in the presence of C59.

overall_design: Balb/c mice (male, 7 week-old, n=6) in each group received 0.2ml  (1 x 109 cells) of strain C59 or strain GG suspension for 2 weeks.

first: Ayako

last: Aoki-Yoshida

first: Reiji

last: Aoki

first: Koko

last: Mizumachi


title: Comparative analysis of gene expression identifies distinct molecular signatures of bone marrow- and periosteal skeletal stem/progenitor cells

status: Public on Dec 08 2017

city: Houston

first: Dongsu

last: Park

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: Genetic comparison between periosteal skeletal stem cells and bone marrow skeletal stem cells in mice

overall_design: Microarray was performed on periosteal derived skeletal stem cells and bone marrow derived skeletal stem cells in Mx1-cre; Ocn-GFP and Mx1-cre; Nestin-GFP mice, respectively. We used Affymetrix array.

first: Lorenzo

last: Deveza


title: Expression data from upper and lower ileum of mice administered lactic acid bacteria, Lactococcus lactis C59 and Lactobacillus rhamnosus GG

summary:
This study aimed to investigate the effects of oral administration of lactic acid bacteria (LAB) on gene expression in murine ileum.
Two LAB strains, Lactococcus lactis subsp. lactis C59 and Lactobacillus rhamnosus GG, were administered to mice for 2 weeks.
Microarray analysis was performed using total RNA from upper and lower ileum to detail the gene expression of 3 groups; control, C59-administered and GG-administered.
Gene expression of upper ileum was less affected by administered strains than that of lower ileum and the latter was strain-specifically affected.


title: Targeting CDK6 and BCL2 exploits the "MYB Addiction" of Ph+ acute lymphoblastic leukemia

status: Public on Jan 17 2018

city: Philadelphia

first: Marco

last: De Dominici

state: Pennsylvania

department: Cancer Biology

institute: Thomas Jefferson University

summary:
Transcriptome analysis of two Ph+ acute lymphoblastic leukemia cell lines after doxycycline induced silencing of MYB.
Current treatment options for Ph+ acute lymphoblastic leukemia (ALL) do not result in long term remission. MYB transcription factor has been shown to be selectively important for Ph+ ALL cell survival and proliferation however the mechanisms for this oncogene addiction are poorly understood and no bona-fide MYB inhibitors currently exist. To overcome these limitations, we analyzed the transcriptome of MYB silenced Ph+ ALL in search for genes regulated by MYB that could serve as potential pharmacological targets. We observed that among MYB-regulated genes, those involved in cell cycle regulation are significantly over-represented. We found that CDK6 and BCL2 are MYB targets pivotal for MYB dependent regulation of proliferation and survival respectively. Furthermore, their inhibition suppresses leukemia growth in vitro and in vivo thus providing a potential treatment approach for patients that fails or do not respond to conventional treatments.

overall_design: Ph+ ALL cells BV173 and SUP-B15 were transduced with the lentiviral vector pLVTSH expressing a MYB-targeting shRNA in a doxycycline inducible manner. Cells were left untreated or treated with doxycycline for 24 h. Then, RNA was extracted from three independent untreated and three doxycycline treated samples and analyzed by microarray.

first: Patrizia

last: Porazzi

first: Angela

last: Soliera

first: Samanta

last: Mariani

first: Sankar

last: Addya

first: Paolo

last: Fortina

first: Luke

middle: F

last: Peterson

first: Orietta

last: Spinelli

first: Alessandro

last: Rambaldi

first: Giovanni

last: Martinelli

first: Anna

last: Ferrari

first: Ilaria

last: Iacobucci

first: Bruno

last: Calabretta


title: Renal carcinoma/kidney progenitor cell chimera organoid as a novel tumorigenesis gene discovery model

status: Public on Dec 05 2017

first: Anatoliy

last: Samoylenko

address: Aapistie 5A

department: FBMM

institute: Oulu University

summary: Three-dimensional (3D) organoids provide a new way to model various diseases, including cancer. We made use of recently developed kidney-organ-primordia tissue-engineering technologies to create novel renal organoids for cancer gene discovery. We then tested whether our novel assays can be used to examine kidney cancer development. First, we identified the transcriptomic profiles of quiescent embryonic mouse metanephric mesenchyme (MM) and of MM in which the nephrogenesis program had been induced ex vivo. The transcriptome profiles were then compared to the profiles of tumor biopsies from renal cell carcinoma (RCC) patients, and control samples from the same kidneys. Certain signature genes were identified that correlated in the developmentally induced MM and RCC, including components of the caveolar-mediated endocytosis signaling pathway. An efficient siRNA-mediated knockdown (KD) of Bnip3, Gsn, Lgals3, Pax8, Cav1, Egfr or Itgb2 gene expression was achieved in mouse RCC (Renca) cells. The live-cell imaging analysis revealed inhibition of cell migration and cell viability in the gene-KD Renca cells in comparison to Renca controls. Upon siRNA treatment, the transwell invasion capacity of Renca cells was also inhibited. Finally, we mixed the nephron progenitors with yellow fluorescent protein (YFP)-expressing Renca cells to establish chimera organoids. Strikingly, we found that the Bnip3-, Cav1- and Gsn-KD Renca-YFP+ cells as a chimera with the MM in 3D organoid rescued, in part, the RCC-mediated inhibition of the nephrogenesis program during epithelial tubules formation. Altogether, our research indicates that comparing renal ontogenesis control genes to the genes involved in kidney cancer may provide new growth-associated gene screens and that 3D RCC-MM chimera organoids can serve as a novel model with which to investigate the behavioral roles of cancer cells within the context of emergent complex tissue structures.

overall_design: Embryonic kidneys were dissected from CD1 embryos at E11.5 and the ureteric bud was removed from the nephron-progenitor/stem-cell-containing MM (Saxén, 1987). The MM cells  were washed twice with cell culture medium, placed on Nuclepore polycarbonate membrane , and a piece of embryonic dorsal spinal cord (E11.5) was glued onto the other filer  side as a robust tubulogenesis inducer. The conjugate was cultured in 37°C, at 5% CO2, for 96 h, snap frozen in liquid nitrogen, and stored at −80°C until used  for RNA purification. Collectively, 40 freshly prepared control and induced MM were processed for the oligonucleotide gene-chip analysis. The analyses were conducted in triplicates.

first: Qi

last: Xu

first: Sanna

last: Junttila

first: Andreas

last: Scherer

first: Jingdong

last: Shan

first: Anatoly

first: Seppo

last: Vainio


title: Smart-seq2 analysis of larval zebrafish habenula from the gng8-GFP transgenic line

status: Public on Mar 23 2018

city: Cambridge

first: Shristi

last: Pandey

address: 16 Divinity Ave

department: Molecular and Cellular Biology

institute: Harvard University

summary: The identification of cell types and marker genes is critical for dissecting neural development and function, but the size and complexity of the brain has hindered the comprehensive discovery of cell types. We combined single-cell RNA-seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula, a conserved forebrain hub involved in pain processing and learning. Single-cell transcriptomes of ~13000 habenular cells (>4x coverage) identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly, despite brain growth and functional maturation, cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions.

overall_design: gng8-GFP zebrafish heads were dissected, dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart-seq2. A total of 22 gng8-GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart-seq2.


title: Inhibition of TGFβRI as a therapy for GATA4 deficient lung cancers [patient samples]

status: Public on Dec 01 2017

city: Beijing

first: huanwei

last: huang

address: 7 Science Park Rd., ZGC life science park

summary: GATA4 is frequently epigenetically silenced in lung cancers. However, the impact of GATA4 inactivation on tumorigenesis and related therapeutic strategy remain to be determined. Through the genome-wide screening of tumor suppressing transcription factors, we demonstrate that GATA4 functions as an essential tumor suppressor in lung cancer in vitro and in vitro. Interestingly, ectopic GATA4 expression resulted in cellular senescence. Mechanistically, GATA4 up-regulates multiple miRNAs (miRNA-32, miRNA-301b, miR-320a, and miR-590) targeting TGFB2 mRNA and causes ensuing downregulation of WNT7B level to induce senescence. TGFBRI inhibitor synergizes with MEK1/2 inhibitor to promote lung cancer regression in Kras G12D/GATA4-/- mouse models. Decreased GATA4 level in clinical specimens negatively correlates with WNT7B or TGFB2 level and is significantly associated with poor prognosis.

overall_design: Compare the mRNA profiles in adenocarcinoma and adjacent tissues  by Illumina suquencing.

first: Liang

last: Chen

first: Lei

last: Gao

first: Huanwei

last: Huang


title: miRNA & mRNA expression data from fractionated SH-SY5Y cells

city: Callaghan

first: Murray

last: Cairns

state: NSW

address: University Drive

institute: University of Newcastle

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

overall_design: Refer to individual Series


title: Acute hemarthrosis in the hemophilia A rat generates a local and systemic pro-inflammatory response

city: Copenhagen

first: Wiktor

last: Majewski

address: Blegdamsvej 9

department: Center for Genomic Medicine

country: Denmark

institute: Copenhagen University Hospital

summary: Replacement therapy with coagulation factor VIII (FVIII) products concurrent with bleeds (on-demand) in hemophilia A (HA) patients, seems to increase the risk for developing anti-drug antibodies (i.e. inhibitors). A danger signal environment characterized by tissue damage and inflammation at the site of a bleed is thought to contribute to the anti-FVIII response. The nature of this inflammatory reaction is however not fully known. The purpose of this study was to characterize the inflammatory response, locally and systemically, during the first 24h following a knee joint bleed in the HA rat. HA rats received either a needle induced knee joint bleed (n=83) or a sham procedure (n=41). Blood samples were collected at selected time-points from 0-24h post injury/sham. Synovial fluid as well as intra-articular knee tissue and popliteal lymph nodes were collected at 24h. Cytokine and chemokine concentrations and mRNA gene expression on tissue samples were measured. Gene expression analysis revealed a rapid inflammatory response in the injured knees, accompanied by significantly increased levels of specific gene products in the synovial fluid; IL-1β, TNFα, KC/GRO, IL-6, Eotaxin, MCP-1, MCP-3, MIP-1α, MIP-2, RANTES, A2M and AGP. Plasma analysis demonstrated significantly increased systemic levels of KC/GRO, IL-6 and AGP in the blood of injured rats, already few hours following the injury. In conclusion, a rapid pro-inflammatory response, both locally and systemically, characteristic of innate immunity, was demonstrated following an induced knee joint bleed in the HA rat. Results reveal a more comprehensive inflammatory picture than previously shown, with resemblance to human hemophilic arthropathy.

overall_design: 20 hemophilia A rats were euthanized 24h after an induced knee joint bleed (n=11) or a sham procedure (n=9). Intra-articular tissue was collected from both knees of the injured rats (injured knee and contralateral knee = 22 samples) and from one knee from the sham/control rat (=9 samples) = 31 samples. Also the popliteal lymph nodes were collected from each of the knees = 31 samples. The collected intra-articular and lymph node tissues were disrupted and homogenized using the TissueLyser II (Qiagen, Hilden, Germany). RNA was purified using the RNeasy® Mini Kit (Qiagen). The purified RNA samples (n=62) were stored at -80°C pending gene expression analysis. The RNA concentration was too low in two of the control rat knee tissue samples, and further gene analysis could therefore not be performed on these. --> 60 samples were used for gene expression analysis: 11 knee tissue + 11 lymph node tissues from injured knees, 11 knee tissue + 11 lymph node from contralateral knees, and 7 knee tissue + 9 lymph node tissue from sham/control knees.

first: Karin

last: Lövgren

first: Olga

last: Østrup