title: Comparative tissue gene expression profiling and alternative splicing by exon-sensitive microarrays in non-syndromic craniosynostosis

status: Public on May 31 2018

city: Rome

first: camilla

last: bernardini

address: L.go F.Vito 1

department: Human Anatomy

institute: UCSC

summary: Craniosynostosis (CS) is the congenital premature fusion of one or more cranial sutures and represents the more prevalent craniofacial malformation in humans, with an overall incidence of 1 out of 2000-3000 live births. Non-syndromic craniosynostoses (NSC) are believed to be multifactorial disorders, with a strong genetic component, due to possible gene–gene or gene–environment interactions that remain to be clearly identified. In this study we delved into the molecular signaling acting in calvarial tissue and cells from patients affected by nonsynodromic midline craniosynostosis, using a comparative analysis between fused and unfused sutures of each affected individuals. Using comparative microarray tissue gene expression profiling we have identified a subset of genes involved in the structure and function of the primary cilium, including the Bardet-Biedl syndrome 9 (BBS9) gene, which was recently associated to sagittal synostosis in a GWAS study. We therefore characterized BBS9 expression and cilium-related signaling in cells isolated from patients’ calvarial bone.

overall_design: 5 patients affected by nonsynodromic sagittal synostosis or nonsyndromic metopic synostosis were enrolled in this study. Tissue specimens were collected, from each patients, both from patent and fused calvarial sutures and cryopreservated in liquid nitrogen. Total RNA was extracted from snap-frozen calvarial tissue specimens using pestel and TRIzol Reagent (Invitrogen), and subsequently purified using silica membrane spin columns from RNeasy Mini kit (Qiagen). The yield, quality and integrity of RNA were determined using the Agilent 2100 Bioanalyzer (Agilent Technologies). The resulting total RNA was then used to created the biotin-labeled library to be hybridized on GeneChip® Exon 1.0 ST human microarrays following the procedure described by the manufacturer (Affymetrix).  The CEL files resulting from the hybridization were analyzed using oneChannelGUI 1.6.5 (Sanges et al. Bioinformatics 2007, 23, 3406-3408).  Exon and gene-level probeset summarization was done by mean of RMA and sketch quantile normalization.  Gene-level differential expression: to assess differential expression at gene-level, we used an empirical Bayes method together with a false discovery rate (FDR) correction of the p-value Thus, the list of differentially expressed genes was generated using an FDR ≤ 0.05 together with an absolute log2(fold-change) threshold of 1.  Exon-level analysis: an intensity filter was subsequently applied at gene-level to remove not expressed and low expressed genes, i.e. genes were retained for exon-level analysis if in all biological replication gene-level signal was greater than 5. Subsequently, only genes characterized to have at least two RNA isoforms annotated in Ensembl database were retained for further analysis. The Splicing Index value was calculated by taking the log2 ratio of the normalized exon intensity (NI) in Sample 1 and the NI in Sample 2. The normalized exon intensity (NI) is the ratio of the probe set intensity to the gene intensity.  Alternative splicing events (ASEs) were detected as described in (Della Beffa et al. BMC Genomics 2008, 9, 571).

first: Marta

last: Barba

first: Camilla

last: Bernardini

first: Lorena

last: Di Pietro

first: Wanda

last: Lattanzi


title: Comparison of gene expressions between LB81 yogurt-intake mice and control mice in the intestine, liver and spleen at 28 months of age

status: Public on Jun 02 2018

city: Tokyo

first: Yuki

last: Usui

state: Tokyo

address: 4-6-1 Shirokanedai, Mintato-ku, Tokyo, Japan

department: Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences

country: Japan

institute: The University of Tokyo

summary:
We performed the long-term administration experiment using a yogurt fermented with Lactobacillus delbrueckii subsp. bulgaricus 2038 and Streptococcus  thermophilus 1131 (LB81 yogurt) for 20 months in order to understand the effects of the long-term intake of probiotics on mice. Microarrays were used to compare the gene expressions of the intestine, liver and spleen tissues between control mice and LB81 yogurt-intake mice at 28 months of age.
Abbreviations used: A, LB81 yogurt-intake mice; C, control mice

overall_design: The eight-month-old ICR male mice obtained from Japan SLC (Hamamatsu, Shizuoka, Japan) were fed on a normal diet (AIN-93) (Oriental Yeast, Tokyo) or the same diet containing 1–2% LB81 yogurt until they were 28 months of age. We isolated the jejunum, ileum, distal colon, liver and spleen tissues from the control mice (n=9) and the LB81 yogurt-intake mice (n=10) at 28 months of age. Equal amounts of total RNA, previously extracted from the tissues of each mouse, were pooled and mixed for each group. The RNA mixtures (100 ng) were individually amplified using the GeneChip 3’IVT Express kit and then hybridized to an Affymetrix Mouse Genome 430 2.0 chip (GPL1261; 45,101 probes).

first: Yasumasa

last: Kimura

first: Takeshi

last: Satoh

first: Naoki

last: Takemura

first: Yasuo

last: Ouchi

first: Hiroko

last: Ohmiya

first: Kyosuke

last: Kobayashi

first: Hiromi

last: Suzuki

first: Satomi

last: Koyama

first: Satoko

last: Hagiwara

first: Hirotoshi

last: Tanaka

first: Seiya

last: Imoto

first: Gérard

last: Eberl

first: Yukio

last: Asami

first: Kosuke

last: Fujimoto

first: Satoshi

last: Uematsu


title: Global expression profiling of hippocampus in a mouse model for Mesio-Temporal Lobe Epilepsy

status: Public on Jun 01 2018

city: Chaidari

first: Despina

last: Sanoudou

address: Rimini 1

department: 4th Department of Internal Medicine

country: Greece

institute: National and Kapodistrian University of Athens

summary:
The Mesio-Temporal Lobe Epilepsy (MTLE) syndrome is the most common form of intractable epilepsies. It is characterized by the recurrence of focal seizures occurring in mesio-temporal limbic structures and is often associated with hippocampal sclerosis and drug resistance.
The aim of this study was to investigate the molecular mechanisms implicated in epileptogenesis in KA-induced MTLE in the mouse, in order to identify novel candidate therapeutic targets.

overall_design: For this purpose, the mouse model for MTLE obtained by intrahippocampal microinjection of kainate (KA;1 nmol/50 nL) was used in parallel with saline-injected animals as controls. The animals were decapitated 6, 12 or 24 hours post injection, the injected hippocampi were dissected and total RNA was extracted. Three RNA pools, from the hippocampi of 3 animals each, were created for each experimental condition (n=9 animals/time-point/treatment). Each pool of RNA was labeled and hybridized to a Mouse Genome 430 2.0 Affymetrix GeneChip.

first: Georgia

last: Kalozoumi

first: Elisavet

last: Vafiadaki

first: Hélène

last: Bernard

first: Antoine

last: Depaulis


title: Transcriptomes comparisons of Dhh KO, Ihh KO and Dhh/Ihh DKO ovaries

status: Public on May 30 2018

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

country: USA

institute: NIEHS

summary: The goal of the microarray analysis is to determine the redundant and distinct roles of Dhh and Ihh in ovarian functions

overall_design: Adult ovaries from 2 months old female mice were used for microarray analysis (Dhh/Ihh Dhet/Control n=8, Dhh KO n=4, Ihh KO n=4, Dhh/Ihh DKO n=3)

first: Chang

last: Liu

first: Humphrey

last: Yao


title: Primary prostate organoid transcriptomic profile in co-culture with primary prostate stroma

city: Chicago

first: Larisa

last: Nonn

state: IL

address: 840 S. Wood St, MC847

department: Pathology

institute: University of Illinois at Chicago

summary: Organotypic in vitro culture is useful to model mammalian disease in numerous tissues. Normal epithelial differentiation and carcinogenesis both undergo in vivo regulation by stroma, but current culture methods exclude stroma. To mimic this in vivo environment, we developed and characterized a human 3D prostate organoid co-culture model that incorporates prostate stroma. Primary prostate stromal cells supported increased organoid formation and expressed growth factors and WNT-related genes involved in epithelial differentiation. Organoid branching occurred distal to physical contact with stromal cells, demonstrating non-random branching. Tumoroids derived from primary prostate cancer maintained differential expression of the prostate cancer marker AMACR only in the presence of stroma. Stroma-induced phenotypes were similar in all patients examined, yet maintained inter-patient heterogeneity in the degree of response. Addition of stroma to in vitro organoid culture recapitulated the in vivo microenvironment by inducing organization of benign organoids into branching structures and preserving prostate cancer phenotypes.

overall_design: 13 samples were analyzed. 7 samples are PrE-3/PrECa-3 and PrE-4/PrECa-4 matched benign/cancer pairs of primary epithelial cells and were cultured in mono or co-culture with PrS (primary stromal cell) mix in 3D conditions. 4 samples are PrS cells isolated from co-culture with PrE-3, PrECa-3, PrE-4, or PrECa-4. 2 samples are RNA isolated from macrodissected tumor from which PrECa-3 and PrECa-4 were derived.

first: Richards

last: Zachary

first: Nonn

last: Larisa


title: Identification of a molecular network of DNA damage-induced neural cell death

status: Public on May 29 2018

city: Baltimore

first: Ted

middle: M

last: Dawson

state: MD

address: 733 N. Broadway, MRB SUITE 731

department: Institute for Cell Engineering

institute: Johns Hopkins University School of Medicine

summary: DNA damage plays a major role in neural cell death by necrosis and/or apoptosis. However, our understanding of the molecular mechanisms of neural cell death remains still incomplete. To acquire a global understanding of the various mediators related to DNA damage-induced neural cell death pathways, we performed a whole genomic wide screen in neural stem cells by using a siRNA library. We identified 80 genes required for DNA damage-induced cell death. 14 genes (17.5%) are directly related to cell death and/or apoptosis. 66 genes have not been previously directly linked to DNA damage-induced cell death. Using an integrated approach with functional and bioinformatics analysis, we have uncovered a molecular network containing several partially overlapping and interconnected pathways and/or protein complexes that are required for DNA damage-induced neural cell death. The identification of the network of neural cell death mediators will greatly enhance our understanding of the molecular mechanisms of neural cell death and provide therapeutic targets for nervous system disorders.

overall_design: The note that new synthesized or activated cell death-inducing proteins are required for DNA damage-induced cell death leads us to propose that cells would be rescued from DNA damage-induced cell death if the cell death-inducing factors were knockdown by siRNAs. To obtain a global understanding of the network of molecular signaling pathways related to DNA damage-induced neural cell death, we performed a whole genome-wide screening using mouse 40k FIV lentiviral small interfering RNA (siRNA) library. We used PCR to amplify siRNA inserts from surviving cells after MNNG (N-methyl-N′-nitro-N-nitrosoguanidine) treatment and reference cells without treatment. The PCR products were labeled with biotin and applied to hybridize with the Affymetrix GeneChip® Mouse Genome 430 2.0 Array to identify surviving cell-associated siRNAs.

first: Jianmin

last: Zhang

first: Zhikai

last: Chi

first: Ying-Min

middle: E

last: Pai

first: Hong

last: Wang

first: Stephen

last: Eacker

first: Valina

middle: L


title: A system of checks and balances: an ERK-dependent feedback mechanism prevents hematopoietic stem cell exhaustion

status: Public on May 28 2018

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

type: Expression profiling by high throughput sequencing

summary: Hematopoietic stem cells (HSC) sustain hematopoiesis throughout life, exiting dormancy to replenish homeostatic or acute cell loss in the peripheral blood. HSC activation is supported by PI3-Kinase/AKT/mTORC1 pathway, which promotes mitochondrial expansion, oxidative phosphorylation, and reactive oxygen species production. Activated HSCs must return to dormancy to prevent exhaustion and bone marrow failure, but the cell-intrinsic mechanisms underlying this transition are unknown. Here we identify an ERK-dependent, rate-limiting feedback mechanism that controls the fitness of the HSC compartment. We show that the MEK/ERK and PI3-Kinase pathways are synchronously deployed in HSC during emergency hematopoiesis, and that feedback phosphorylation of MEK1 by activated ERK is required to constrain AKT/mTORC1 activation. Genetic or chemical ablation of this feedback tilts the balance between HSC dormancy and activation, increasing the output of differentiated cells and accelerating HSC exhaustion. MEK inhibitors developed for cancer therapy may thus be useful to modulate HSC activation.

overall_design: RNA-seq: WT (n=3+1 technical) vs. KO (n=3) HSCs + 5-FU-treated WT (n=4) vs. KO (n=3) HSCs; 13 RNA-seq datasets total

first: Christian

last: Baumgartner

first: Stefanie

last: Toifl

first: Matthias

last: Farlik

first: Florian

last: Halbritter

first: Ruth

last: Scheicher

first: Irmgard

last: Fischer

first: Veronika

last: Sexl

first: Manuela

last: Baccarini


title: Affymetrix CytoScan HD for autism spectrum disorder in children

status: Public on May 25 2018

city: Olomouc

first: Josef

last: Srovnal

address: Hnevotinska 5

department: IMTM

country: Czech Republic

institute: Palacky University

type: Genome variation profiling by genome tiling array

summary: Autism spectrum disorder (ASD) is a complex heterogeneous developmental disease with a significant genetic background that is frequently caused by rare copy number variants (CNV). The aim of the study was to identify new candidate genes for ASD in the studied cohort of ASD-diagnosed patients. We used chromosomal microarray analysis (CMA) - a Cytoscan HD (Affymetrix, Santa Clara, CA, USA) to detect CNV in 87 ASD patients and their relatives and evaluated their clinical significance. Pathogenic and likely pathogenic mutations were identified by CMA in 8 and 9 ASD patients, respectively. CMA revealed 89 rare CNV: 8 pathogenic, 12 designated VOUS - likely pathogenic, 12 VOUS - uncertain, and 57 VOUS - likely benign or benign. CNV (pathogenic/VOUS-likely pathogenic/VOUS - uncertain) overlapping the same gene in more than one patient were observed in DOCK8 gene and PARK2 gene. This work presents new evidence about the possible roles of PARK2 and DOCK8 in the etiology of ASD, and suggests CTNNA2 as a candidate gene for ASD risk.

overall_design:
Affymetrix CytoScan HD arrays were performed according to the manufacturer's directions on DNA extracted from peripheral blood samples.
Copy number analysis of Affymetrix CytoScan HD arrays was performed for 87 ASD patients and their relatives.

first: Pavlina

last: Capkova


title: Effect of a progressive weaning on behavioural and physiologic indicators in foals (Equus caballus)

city: Bordeaux

first: Aline

last: FOURY

address: 146 rue Léo Saignat

country: France

institute: INRAE

summary: The weaning process has been identified as being associated with stress, weight loss and stereotypies. To limit these problems, some breeders wean the foals gradually. This article presents the effects of a progressive weaning on various physiological parameters (cortisol, C reactive protein, length of telomeres) and on the blood transcriptome, among the foals and the mares. Results indicate that a progressive weaning has beneficial short-term effects in foals, and that in the longer term the foals weaned abruptly have compensated this gap. In mothers, the beneficial effects of the progressive weaning are less important.

overall_design: Gene expression induced by weaning conditions in horse blood was measured in foals 30 days (D30) and 95 days (D95) after the weaning. There were 16 samples for the brutal weaning (B) and 16 samples for the progressive weaning (P).

first: Marie

middle: P

last: Moisan

last: Foury

first: Léa

last: Lansade


title: Effect of a progressive weaning on behavioural and physiologic indicators in mares (Equus caballus)

overall_design: Gene expression induced by weaning conditions in horse blood was measured in mares 30 days after the weaning. There were 16 samples for the brutal weaning (B) and 16 samples for the progressive weaning (P).


title: Whole skin treated with Ruxolitinib, tofacitinib or vehicle control for 4 days

status: Public on May 27 2018

city: New York

first: Jane

middle: E.

last: Cerise

state: NY

address: 1150 St. Nicholas Avenue

institute: Columbia University

summary:
Day 0= whole skin from C57/B6 female at 8.5 weeks of age
Day5= whole skin from C57/B6 female after 4 days of treatment with vehicle, ruxolitinib or tofacitinib

overall_design: Mice were biopsied at day 0, treated with respective topical drugs daily for 4 days, and biopsied again at day 5. Control and treatment samples are paired

first: Sivan

last: Harel

first: Angela

last: Christiano


title: Effect of a progressive weaning on behavioural and physiologic indicators in foals and mares (Equus caballus)

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

overall_design: Refer to individual Series


title: Murine mammary gland: PRA transgenics vs. wild-type

status: Public on May 23 2018

first: Maria

middle: Jose

last: Carlini

department: Neurology

summary: Progesterone receptor (PR) is expressed from a single gene as two isoforms, PRA and PRB. In normal breast human tissue, PRA and PRB are expressed in equimolar ratios, but isoform ratio is altered during malignant progression, usually leading to high PRA:PRB ratios. We took advantage of a transgenic mouse model where PRA isoform is predominant (PRA transgenics) and identified the key transcriptional events and associated pathways underlying the preneoplastic phenotype in mammary glands of PRA transgenics as compared with normal wild-type littermates.

overall_design: Reference-based 2-color microarray design. Two-condition experiment, PRA transgenics vs. wild-type. Biological replicates: 3 wild-type, 4 PRA transgenics.

middle: J


title: Transcriptome profiling of endothelial cells from wild-type, hhex mutants and hhex-overexpression zebrafish embryos

status: Public on May 17 2018

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

summary: We used high throughput sequencing to identify differential expression in siblings, hhex mutants and hhex-overexpression endothelial cells at 48 hpf.

overall_design: FACS sorted endothelial cells from siblings, hhex mutants and hhex-overexpression at 48 hpf

first: Sébastien

last: Gauvrit

last: Guenther


title: Early isolated v-lesion may not truly represent a rejection of kidney allograft

status: Public on May 22 2018

city: Praha 4

first: Petra

last: Hruba

address: Videnska 1958

department: Transplant Laboratory

institute: Institute for Clinical and Experimental Medicine

summary: Intimal arteritis is known to be a negative prognostic factor for kidney allograft survival. Although Banff classification assesses isolated v-lesion (IV) as a T-cell mediated rejection, its origin and significance remain unclear. To help resolve if IV truly represents acute rejection, molecular study was performed.  Transcriptome of early IV, T cell-mediated vascular rejection (TCMRV) and nonrejection histologic findings was compared using microarrays (Illumina Human HT-12 v4 Expression BeadChips). The enrichment of deregulated genes was analysed using DAVID.   Differential gene expression analysis identified 310 genes to be deregulated in TCMRV compared to IV. Gene enrichment analysis categorized deregulated genes to be associated with immune and inflammatory response. Principal component and unsupervised hierarchical cluster analysis revealed clear distinction of TCMRV samples but showed similarity of IV with control group. RT-qPCR validation on external sample set (n=20) confirmed upregulation of genes involved in immune response in TCMRV compared to IV. Based on stepwise logistic regression SLA2 gene represented the strongest group classifier [OR 0.106 (95 % CI 0.01- 0.774), p=0.03] with ROC AUC 0.906 [95% CI (0.769-1.0), p=0.003)].   IV reveals weak immunologic signature compared to TCMRV but shows similarity with non-rejection findings. Early IV in a DSA- and C4d- negative patients may feature non-rejection origin and reflect injury distinct from alloimmune response. Study calls for reassessment of current Banff histopathology criteria which considers an intimal arteritis to be TCMR irrespective of TI and supports use of molecular diagnostics as a part of integrative approach.

overall_design: An observational, retrospective, cohort study was performed to compare expression profiles of renal allograft biopsies with histologic findings of TCMRV and IV. IV was defined as an intimal arteritis (v>0) with minimal tubulitis and interstitial inflammation (t<2, i<2), no microvascular inflammation [glomerulitis (g)+ peritubular capilaritis (ptc)=0], with C4d and DSA negativity (n=6). TCMRV was defined as presence of intimal arteritis with significant TI (t>1, i>1) in the absence of C4d and DSA positivity and served as positive control (n=4). Only indication kidney allograft biopsies performed due to graft nonfunction or function deterioration within first month after kidney transplantation were included. As a negative control group, normal histologic findings in 3 months protocol biopsies (C4d negative, no signs of rejection, DSA negative) with no history of previous rejection were included (n=8). As microarray platform,  Illumina HumanHT 12 v4.0 Expression BeadChips (Illumina) was used.

first: Mariana

last: Wohlfahrtova

first: Jiri

last: Klema

first: Marek

last: Novotny

first: Zdenek

last: Krejcik

first: Viktor

last: Stranecky

first: Eva

last: Honsova

last: Vichova

first: Ondrej

last: Viklicky


title: Transcriptional profiles of miR-155 overexpressing CD8T cells during chronic infection

status: Public on May 16 2018

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

state: PA

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

institute: University of Pennsylvania

summary: Persistent viral infections and tumors drive development of exhausted T (TEX) cells. In these settings, TEX cells establish an important host-pathogen or host-tumor stalemate. However, TEX cells erode over time, leading to loss of pathogen or cancer containment. We identified microRNA (miR)-155 as a key regulator of sustained TEX cell responses during chronic lymphocytic choriomeningitis virus (LCMV) infection. Genetic deficiency of miR-155 ablated CD8 T cell responses during chronic infection. Conversely, enhanced miR-155 expression promoted expansion and long-term persistence of TEX cells. However, rather than strictly antagonizing exhaustion, miR-155 promoted a terminal TEX cell subset. Transcriptional profiling identified coordinated control of cell signaling and transcription factor pathways, including the key AP-1 family member Fosl2. Overexpression of Fosl2 reversed the miR-155 effects, identifying a link between miR-155 and the AP-1 transcriptional program in regulating TEX cells. Thus, we identify a mechanism of miR-155 regulation of TEX cells and a key role for Fosl2 in T cell exhaustion.

overall_design:
RNA-Seq analysis was used to investigate how miR-155 affects the expansion and differentiation of CD8 Tcells during chronic infection
12 samples from 4 groups, 3 replicates each

first: ERIETTA

last: STELEKATI

last: Wherry


title: Gene expression from mouse lung adenocarcinoma-associated macrophages

city: Frederick

first: NA-YOUNG

last: SONG

address: 1050 Boyles Street

institute: NCI

summary: Comparison of gene expression of mouse lung adenocarcinoma-associated macrophages isolated from C57BL/6 mice injected with Kras-CL and Kras IKKa low cells

overall_design: Lung tissues were collected at 1.5 months after cell injection. Then macrophages were isolated and culutred on the plates. Total RNAs from macrophages were extracted using Trizol and then subjected to hybridization for Affymetrix microarray.

first: Song

last: Na-Young

first: Hu

last: Yinling


title: Genome-wilde expression profiling analysis of yeast cells lacking the decapping activator Scd6

status: Public on May 15 2018

city: Worcester

first: Feng

last: He

state: MA

address: 368 Plantation Street

department: Microbiology and Physiological Systems

institute: University of Massachusetts Medical School

summary: To assess the role of the decapping activator Scd6 in mRNA decay, we used RNA-Seq to analyze the expression profile of yeast cells harboring a deletion of the SCD6 gene. Consistent with our recent model for decapping regulation, we found that Scd6 targets a small number of specific mRNAs in yeast cells. Interestingly, degradation of Scd6-targeted transcripts also requires the functions of the decapping activators Pat1, Lsm1, and Dhh1, suggesting that Scd6 functions together with Pat1, Lsm1, and Dhh1 in promoting mRNA decapping.

overall_design: Genome-wide expression profiles of the wild-type and scd6∆ strains were generated by RNA-Seq, in triplicate, using Illumina HiSeq4000. Transcripts differentially expressed in the scd6∆ strain were identified by comparing to the wild-type strain.

first: Allan

last: Jacobson


title: Transcriptomic profiling of C57BL/APC-KO mice after 9 months treatment with Phenobarbital

city: Basel

first: Jonathan

last: Moggs

address: Fabrikstrasse 2

country: Switzerland

institute: Novartis

summary: In rodent liver, a single injection of N-nitrosodiethylamine (DEN) followed by chronic treatment with the antiepileptic drug phenobarbital (PB) promotes the outgrowth of hepatocellular tumors with activating mutations in Ctnnb1, encoding the transcription factor β-catenin. We now studied long-term effects of PB treatment in livers of transgenic mice with hepatocyte-specific knockout (KO) of Apc, a negative regulator of β-catenin signaling. The number of Apc KO hepatocytes present in the liver decreased with age, indicative of a selective disadvantage of Apc KO cells in the absence of PB. Following liver tumor promotion by PB in Apc KO mice for 9 months, tumor burden was quantified and histological appearance, gene expression profiles, and activity of oncogenic signaling pathways of the tumors were analyzed. In Apc KO mice fed with PB, we observed an increased hepatic tumor volume fraction and tumor multiplicity, as compared to non-promoted animals. Tumors in the PB-treated Apc KO group were mostly eosinophilic hepatocellular adenoma with activated β-catenin, due to the deletion of Apc. These tumors exhibited striking phenotypic similarities to DEN-induced Ctnnb1-mutated tumors, regarding histological appearance and expression of marker proteins and mRNAs. A particular sub-population of tumors, Apc KO-driven basophilic hepatocellular carcinomas, exclusively appeared in the non-PB-treated group but was absent from PB-promoted livers. In conclusion, phenobarbital promotes the outgrowth of Apc-deficient, β-catenin-activated hepatocellular adenoma while simultaneously inhibiting the formation of a certain population of Apc-driven hepatocellular carcinoma.

overall_design: 6 weeks old male C57BL mice with a triggerable APC knockout received a tumor initiation dose of DEN prior to 9 months of treatment with or without 0.05% Phenobarbital. We profiled mRNA expression in liver tissue to assess the effects of the APC knockout on tumor development with PB.

first: Albert

last: Braeuning

first: Michael

last: Römer

last: Schwarz


title: Transcriptomic profiling of liver of Ctnnb1-KO and WT mice after 12 weeks exposure to Phenobarbital (mRNA)

status: Public on May 11 2018

summary: Signaling through the Wnt/b-catenin pathway is a crucial determinant of hepatic zonal gene expression, liver development, regeneration, and tumorigenesis. The gene encoding b-catenin is called Ctnnb1. We have previously shown, that liver tumour promotion mediated by the model tumour promoter phenobarbital (PB) is completely lost in mice, where Ctnnb1 has been conditionally knocked out in hepatocytes (CTNNB1KO mice; Rignall et al., Carcinogenesis 32, 52-57, 2010). In the present study, the effect of a 12 weeks PB exposure on the liver miRNA expression pattern was  investigated, in order to potentially get information on the nature of the loss of promotional activity in the CTNNB1KO mice.

overall_design: For animal used and experimental details see Baeuning et al., Histochem. Cell Biol 134, 469-481, 2010.


title: Comparison of gene expression in macrophages tolerised by different toll-like receptor ligands

city: St. Lucia

first: Othmar

last: Korn

state: Queensland

address: University of Queensland

country: Australia

institute: Australian Institute for Bioengineering and Nanotechnology

summary: To investigate the similarity of toll-like receptor tolerance in macrophages stimulated with different toll-like receptor ligands we stimulated naïve or tolerant macrophages with ligands for TLR4, TLR2, TLR3 and TLR9. The data identifies a core set of genes that are tolerised by all ligands and genes that show TLR specific patterns.

overall_design: Bone marrow derived macrophages were stimulated with four different toll-like receptor ligands; LPS, CpG, Pam3csk4 and PolyI:C. In addition some cells received a pre-treatment with the same ligand prior to restimulation to induce a tolerant state. Gene expression was measured at 4 hours post stimulation with each ligand. Three independent experiments were performed to measure gene expression changes between each macrophage group. Of the 27 samples, LPSTolerance_3 and Pam3csk4_2 were excluded from the analysis entirely due to low sample quality – they are included in this dataset for completeness only.

first: Ruaidhri

last: Carmody


title: Identification of SoxC-regulated genes during neurogenesis in the developing spinal cord

status: Public on May 10 2018

city: Erlangen

last: Wegner

state: Bavaria

address: Fahrstr. 17

department: Institut of Biochemistry

sample_organism:
Gallus gallus
Mus musculus

platform_organism:
Gallus gallus
Mus musculus


title: Identification of SoxC-regulated genes during neurogenesis in the developing spinal cord [mouse]

summary:
The HMG-domain containing SoxC transcription factors Sox4 and Sox11 are expressed in the vertebrate central nervous system in neuronal precursors and neuroblasts. They are required during early stages of neurogenesis.
Here we perform micorarray analysis to identify genes that are downstream of these SoxC proteins during spinal cord neurogenesis in mouse. The identified genes represent potential direct target genes of Sox4 and Sox11.

overall_design: Total RNA was prepared from brain of wildtype and Sox4/Sox11-double deficient mouse embryos at day 14.5 of embryogenesis and used to compare overall gene expression patterns between the two genotypes using Affymetrix microarrays.

first: Franziska

last: Fröb

first: Elisabeth

last: Sock


title: De novo formation of a functional biliary system by TGFβ-mediated hepatocyte transdifferentiation

status: Public on May 14 2018

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

summary: We observed de novo formation of peripheral bile ducts by transdifferentiation of hepatocytes in mice born without peripheral bile ducts. To assess the authenticity and maturity of the hepatocyte-derived peripheral cholangiocytes forming the new bile ducts, we compared their global gene expression profile to that of peripheral cholangiocytes isolated from normal mice. We also included hepatocytes isolated from mice born without peripheral bile ducts as a control.

overall_design: We isolated hepatocyte-derived peripheral cholangiocytes, peripheral cholangiocytes and hepatocytes from mouse livers by FACS, extracted RNA and performed RNA-seq, using single end 50bp reads.

first: Holger

last: Willenbring

first: Johanna

middle: R

last: Schaub

first: Simone

middle: N

last: Kurial

middle: A

first: Stacey

middle: S

last: Huppert


title: Exon level expression analysis from rhabdomyosarcoma patient tumors.

status: Public on May 18 2018

city: Columbus

first: Genevieve

last: Kendall

address: 700 Children's Drive, WA5014

institute: Nationwide Children's Hospital / The Ohio State University

summary: Rhabdomyosarcoma is a childhood tumor with features of aberrant muscle differentiation. We studied samples from 101 rhabdomyosarcoma patients to determine core gene expression signatures relevant in the disease.

overall_design: 101 rhabdomyosarcoma patient samples were analyzed with the Human Exon 1.0 ST Array from Affymetrix.

first: Tim

last: Triche

first: Stephen

last: Skapek


title: Bhlhe40 is an essential repressor of IL-10 during Mycobacterium tuberculosis infection

status: Public on May 09 2018

city: St. Louis

first: Maxim

last: Artyomov

state: MO

address: 425 S Euclid Ave

department: Pathology and Immunology

institute: Washington University in St. Louis

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The cytokine IL-10 antagonizes pathways that control Mycobacterium tuberculosis (Mtb) infection. Nevertheless, the impact of IL-10 during Mtb infection has been difficult to decipher because loss of function studies in animal models have yielded only mild phenotypes. We have discovered that the transcription factor Bhlhe40 is required to repress Il10 expression during Mtb infection. Loss of Bhlhe40 in mice results in higher Il10 expression, higher bacterial burden, and early susceptibility similar to that observed in mice lacking IFN-g. Deletion of Il10 in Bhlhe40-/- mice reverses these phenotypes. Bhlhe40 deletion in T cells or CD11c+ cells is sufficient to cause susceptibility to Mtb. Bhlhe40 represents the first transcription factor found to be essential during Mtb infection to specifically regulate Il10 expression, revealing the importance of strict control of IL-10 production by innate and adaptive immune cells during infection. Our findings uncover a previously elusive but significant role for IL-10 in Mtb pathogenesis.

overall_design: Bhlhe40+/+ and Bhlhe40-/- GM-CSF-cultured bone marrow-derived cells were stimulated in the presence of 10 µg/ml heat-killed Mycobacterium tuberculosis (H37Ra strain, Difco) for 4 hours. Bhlhe40+/+ and Bhlhe40-/- in vitro-polarized TH1 cells were stimulated with PMA (50 ng/ml, Enzo Life Sciences) and ionomycin (1 µM, Enzo Life Sciences) for 1.5 hours. After stimulation, cells were fixed and genomic DNA was immunoprecipitated with anti-Bhlhe40 antibody.

first: Jeremy

last: Huynh

first: Chih-Chung

last: Lin

first: Jacqueline

last: Kimmey

first: Nicholas

last: Jarjour

first: Elizabeth

last: Schwarkopf

first: Tara

last: Bradstreet

first: Irina

last: Shchukina

first: Oleg

last: Shpynov

first: Casey

middle: T

last: Weaver

first: Reshma

last: Taneja

first: Brian

last: Edelson

first: Christina

last: Stalling


title: Gene expression in CD8 vs. CD8+Cho cells

status: Public on May 03 2018

city: Houston

first: xingzhe

last: ma

state: TX

address: 6565 fannin street

department: cancer center

institute: houston methodist hospital

summary: Gene expression in in vitro differentiated CD8 T cells and CD8 T cells treated with cholesterol.

overall_design: Compare gene expression difference in CD8 vs. CD8+Cho cells.

first: Xingzhe

last: Ma


title: Gene expression signatures for B cells from tumor draining lymph node and normal lymph node

status: Public on May 01 2018

city: Shanghai

first: Liu

last: Yanfang

address: 800 Xiangyin Road

department: Immunology

country: China

institute: Second Military Medical University

summary: To determine the different gene signatures between B lymphocytes from tumor draining lymph node (DLN) and normal lymph node (NLN), we have employed gene microarray as a discovery platform to identify gene signatures of tumor-educated B cells in DLN from tumor-bearing mice, taking NLN from normal mice as a control. We subcutaneously inoculated Balb/c mice with breast cancer cell line 4T1. Two weeks later, DLN was harvest and B cells were purified as descript in “treatment protocol”. From gene microarray, we found that B cells in DLN showed quite different transcript profiles from that in NLN.

overall_design: Examination of different gene signatures between B cells from tumor draining lymph node and normal lymph node

first: Xuetao

last: Cao

first: Yan

last: Gu


title: Global gene expression profiling reveal distinct molecular profiles between p53-sensitive and p53-resistant T-cell lymphomas

city: Smithville

first: Bin

last: Liu

address: 1808 Park Road 1C

department: Epigenetics and Molecular Carcinogenesis

institute: University of Texas MD Anderson Cancer Center

summary:
TP53 mutations occur in approximately 50% of all human tumors with increased frequency in aggressive cancers that are notoriously difficult to treat. Additionally, p53 missense mutations are remarkably predictive of refractoriness to chemo/radiotherapy in various malignancies. These observations have led to the development of mutant-p53 targeting agents that restore p53 function. An important unknown is which p53-mutant tumors will respond to p53 reactivation-based therapies. Here we found a heterogeneous impact on therapeutic response to p53 restoration, suggesting it will unlikely be effective as a single therapy.
The goal of the study was to identify the pathways conferring resistance or sensitivity to genetic p53 restoration in tumors with a p53 missense mutaiton
Results:We sequenced the transcriptome of tumors that were sensitive or resistant to p53 restoration and found that TNF signaling was activated in p53-sensitive tumors.

overall_design: 12 independent biological samples were analyzed to compare tumors that were sensitive (n=8) or resistant (n=4) to genetic p53 restoration

first: Guillermina

last: Lozano

first: Connie

last: Larsson


title: Cleavage Factor 25 Deregulation Contributes to Pulmonary Fibrosis through Alternative Polyadenylation

city: Irvine

first: Lei

last: Li

state: CA

address: University of California, Irvine

institute: University of California, Irvine

summary: The purpose of this experiment is to identify the APA targets of CFIm25 in human lung fibroblasts.   Following the knockdown of CFIm25 in normal human lung fibroblasts, we identified 808 genes with shortened 3’UTRs, including those involved in the transforming growth factor-beta signaling pathway, the Wnt signaling pathway, and cancer pathways.

overall_design: mRNA profiles of primary human lung fibroblasts transfected with control or CFIm25 siRNA were generated by RNA-Seq using Illumina GAIIx

first: Tingting

middle: W

last: Mills

first: Zheng

last: Xia

first: Wei

first: Eric

last: Wagner

first: Michael

last: Blackburn


title: Expression data of different regions of E11.5 mouse optic cups

city: Guangzhou

first: SHUYI

last: CHEN

state: Guangdong

address: 54 S. Xianlie Rd

department: State Key Laboratory of Ophthalmology

institute: Zhongshan Ophthalmic Center, SYSU

summary: Optic fissue is a transient opening on the ventral side of developing optic cup. Failure in optic fissue closure will cause coloboma formation. The aim of this study was to compare optic fissue transcriptome with center optic cup to find optic fissue specific genes.

overall_design: optic fissue, nasal- and temporal regions of the Optic cups of E11.5 mouse embryos was microdissected using laser-assisted microdissection. Total RNAs were extracted and processed to cRNA library and hybridized to Affymetrix mouse genome 4302.0 arrays. Each region has three biological replicates.

first: Shuyi

last: Chen


title: Acetate and B cells

status: Public on Apr 30 2018

city: West Lafayette

first: Chang

last: Kim

state: IN

address: 725 Harrison St

department: Comparative Pathobiology

institute: Purdue

summary:
Mouse spleen B cells were activated with sodium acetate (10 mM) for 5 days and the transcriptome change was determined with microarrays.
This experiment determines the effect of acetate on gene expression in B cells.

overall_design: Spleen CD19+ B cells were activated with  blank or sodium acetate (10 mM) for 5 days. The transcriptome was determined with Mouse 430 2.0 chips (Affymetrix, Inc.).

middle: H

first: Yaqing

last: Qie


title: Circular RNA expression alteration in rats after traumatic spinal cord injury (SCI)

city: Beijing

first: Chuan

last: Qin

address: No.95,yong an road.

department: Department of Urology

institute: Beijing Friendship Hospital, Capital Medical University

summary: To determine whether the expression levels of circular RNAs were altered and lay a foundation for future work, we used high-throughput microarray analysis to screen circular RNAs expression patterns in the spinal cord of adult rats after traumatic spinal cord injury (SCI), finally to evaluate the potential rat models as a platform for the development of novel therapeutic targets for spinal cord injury in future clinical studies. Overall six rats at 3 days post-SCI in two groups were used to perform the microarray.

overall_design: Six rats were randomly assigned to two groups: rats in the sham control group (n=3) were treated with laminectomy alone without contusion; rats in the SCI group (n=3) were subjected to laminectomy plus contusion. Rats were anesthetized at 3 days post-SCI, and a 1cm long segment of spinal cord, including the injury epicenter, was dissected and collected for the experiment.

first: Jian-Jun


title: Differences in metabolic biomarkers in the blood and gene expression profiles of peripheral blood mononuclear cells among normal weight, mildly obese, and moderately obese subjects

city: Daegu

first: Un Ju

last: Jung

address: 1370, Sankyuk-dong, Buk-gu

department: Center for Food & Nutritional Genomics

country: South Korea

institute: Kyungpook National University

summary: Objectives: We compared metabolic biomarkers in the blood and PBMC gene expression profiles among normal weight, mildly obese, and moderately obese Korean adult men.  Design: Subjects were classified as normal weight (BMI, 18.5~23 kg/m2), mildly obese (BMI, 25~27.5 kg/m2), and moderately obese (BMI, 27.5~30 kg/m2).  Results: High leptin, lipids (except LDL- and HDL-cholesterol), and apolipoprotein B levels and low adiponectin and HDL-cholesterol levels were present in the plasma of both mildly and moderately obese subjects. Circulating levels of inflammatory cytokines (TNF-α and IL-6) and markers of insulin resistance, oxidative stress, and liver damage were altered in moderately obese subjects but not mildly obese subjects. PBMC transcriptome data showed enrichment of pathways involved in energy metabolism, insulin resistance, bone metabolism, cancer, inflammation, and fibrosis in both mildly and moderately obese subjects. Signaling pathways involved in oxidative phosphorylation; triglyceride synthesis; carbohydrate metabolism; insulin, mTOR, FOXO, RAP1, RAS, and TGF-β signaling; and ECM–receptor interaction were enriched only in moderately obese subjects, indicating that changes in PBMC gene expression profiles according to metabolic disturbances were associated with the development and/or aggravation of obesity. In particular, upregulation of 8 genes (FLT3LG, LTB, IL23A, CD19, CPT1B, AXIN2, CACNA1L, RPRM) and downregulation of 2 genes (CCL4L1, LPAR5) were observed only in mildly obese subjects. Six genes (CXCR5, NFKBIA, BIRC3, TNFAIP3, DDIT3, PDE4B) and 4 genes (CX3CR1, HSPA1A, CACNA2D3, APAF1) were up- and down-regulated, respectively, in both mildly and moderately obese subjects. These results suggested that these genes could be used as early or stable biomarkers for diagnosing and treating obesity-associated metabolic disturbance.

overall_design: Total RNA of peripheral blood mononuclear cells was obtained from normal weight (BMI, 18.5~23 kg/m2), mildly obese (BMI, 25~27.5 kg/m2) and moderately obese (BMI, 27.5~30 kg/m2) subjects and mRNA expression was measured using microarray analysis.

first: Un

first: Myung-Sook

last: Choi


title: Transcriptional profiling of CD1 mouse liver after 28 days and 90 days of daily administration of Phenobarbital in vivo

status: Public on Apr 27 2018

first: Jonathan

last: Moggs

summary: To further our investigations for early biomarkers of non-genotoxic carcinogenesis, groups of mice were treated by gavage with a prototypic non-genotoxic carcinogen: Phenobarbital (PB, CAS: 57-30-7), for a period of 28 and 90d and liver tissue harvested for expression profiling. Control groups were treated with appropriate vehicle (0.5% Methylcellulose).

overall_design: Group size was 5 mice (mus musculus, CD1, randomly assigned); all procedures were performed by experienced personnel.

first: Nina

last: Ostenfeldt

last: Römer

first: Heidrun

last: Ellinger-Ziegelbauer

first: Dorthe

middle: B

last: Thomsen


title: 10x analysis of wild-type (TLAB) and MZoep zebrafish embryos at 6-somite stage

city: Bethesda

first: Jeffrey

middle: Allen

last: Farrell

address: 6 Center Drive (6A/1A06)

department: Division of Developmental Biology

institute: National Institute of Child Health and Human Development

summary: Wild-type and MZoep zebrafish embryos were mechanically dissociated and profiled using 10x Genomics pipeline.

overall_design: 10x scRNA-seq was performed on visually staged, mechanically dissociated embryos. Samples were combined and sequenced in one batch.

first: Yiqun

last: Wang


title: mRNA profiles of WT and STAT6-/- mice colon tissue

status: Public on Apr 24 2018

first: Yuli

last: Lin

address: No.130, Dong'an Road, Xuhui

institute: Fudan University

summary: Colon tissues from 6-8 week BALB/c mice and STAT6-/- mice having 3% DSS for 3 days were obtained. Total RNAs were isolated with Trizol (invitrogen) and the RNA-seq library was prepared by the Beijing Genomics Institute. Sequence reads were obtained using BGIseq500 and successfully mapped to mouse genome. Reads counts were normalized based on FPKM, fold changes were calculated for all possible comparisons.

overall_design: Gene expression of colon tissue of 3% DSS treated WT and STAT6-/- mice


title: small-RNA-Seq in human T-cell lymphoblastic lymphoma samples and control thymuses

status: Public on Apr 25 2018

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

country: Spain

institute: CNIO

type: Non-coding RNA profiling by high throughput sequencing

summary: Precursor T-cell lymphoblastic neoplasms are aggressive haematological neoplasm that most often manifest with extensive marrow and blood affectation (T-cell acute lymphoblastic leukaemia or T-ALL) or less commonly as a thymic mass with limited bone marrow infiltration (T-cell lymphoblastic lymphoma or T-LBL). Here we show data from small-RNA-Seq in a sample series of T-LBL from Spanish patients.The goal was to determine the levels of expression of coding genes and microRNAs, and to identify all genetic variants including SNVs, indels, and fusion transcripts.

overall_design: Expression data were determined by comparson of each tumour sample with two control thymuses (404 and 405). Genetic variants were determined by comparison of tumour sequences with canonical ENSEMBL normal-references of each gene.

first: Jose

last: Fernandez-Piqueras

first: Pablo

middle: F

last: Navarro

first: Pilar

last: Nieva

first: Maria

middle: V

last: Morales

first: Marcos

last: Malumbres


title: Comparison of transcriptomic profiles in the skeletal muscle of control and constitutive thin subjects

status: Public on Apr 20 2018

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

summary: Skeletal muscle biopsies were taken from either control female subjects or constitutive thin female subjects.

overall_design: Skeletal muscle biopsies from 8 constitutive thin patients and 8 control subjects were taken for RNA extraction and hybridization on Affymetrix  Human Exon 1.0 ST arrays  to characterize the transcriptomic profile of this specific type of patients

first: Emmanuelle

last: Meugnier

first: Natacha

last: Germain-Zito

first: Sandra

last: Pesenti

first: Hubert

last: Vidal

first: Bruno

last: Estour


title: Antibacterial mode of action of alpha-mangostin on Staphylococcus epidermidis

status: Public on Apr 19 2018

city: Helsinki

first: Päivi

last: Saavalainen

address: Haartmaninkatu 8

department: TRIMM

country: Finland

institute: University of Helsinki

summary: Alpha-mangostin (α-MG) is a natural xanthone reported to exhibit rapid bactericidal activity against Gram-positive bacteria, and may therefore have potential clinical application in healthcare sectors. This study sought to identify the antibacterial mode of action of α-MG against Staphylococcus epidermidis RP62A through RNA-sequencing technology.

overall_design: Overnight cultures of S. epidermidis were diluted 1:100  in LB and were grown to mid-log at 37 °C. Bacterial cells were treated with 0.7 MIC (0.875 µg/ml) of α-MG or 0.1 % methanol (solvent control) for 10 min. After incubation, bacterial total RNA was isolated. Samples were prepared in triplicates. The ribosomal RNA was depleted using Ribo-Zero rRNA Removal kit for Gram-positive bacteria. Sequencing library was prepared using the drop-seq protocol (Macosko et al., 2015) with specially designed random hexamer-based capture oligos with known barcodes. Paired-end sequencing was performed on NextSeq500 sequencer (Illumina) in FuGU (Helsinki, Finland).

first: Katarzyna

last: Leskinen

first: Murugesan

last: Sivaranjani


title: Genome-wide maps of linker histone H1 lysine 85 acetylation in HCT116 cells

status: Public on Apr 18 2018

first: Zhiming

last: Li

state: Beijing

address: Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences

institute: Peking University Health Science Center

summary: We identify acetylation of linker histone H1 lysine 85 as a novel histone acetylation mark, which regulates chromatin structure and genome stability upon DNA damage. By performing a chromatin immunoprecipitation and deep sequencing assay, we identified the genome-wide distribution patterns of H1 lysine 85 acetylation in HCT116 cells. We found that H1K85ac largely bound intergenic regions (53%) and gene bodies (39%), whereas only 7% H1K85ac bound regions 2 kb upstream of the transcription start sites (TSSs). As the proportion of H1K85ac bound to potential promoter regions was not significantly different to that of the random peaks (~6%), these data suggest that H1K85ac may not be mainly involved in general transcriptional regulation.

overall_design: Examination of H1 lysine 85 acetylation in HCT116 cells

first: Yinglu


title: GPR68 senses flow and is essential for vascular physiology

city: San Diego

first: John

last: Walker

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

summary: GPR68 is an essential flow sensor in arteriolar endothelium, and is a critical signaling component in cardiovascular pathophysiology

overall_design: RNAseq of cells from mesenteric endothelium of mice plus and minus GPR68

first: Jie

last: Xu

first: Jayanti

last: Mathur

first: Emilie

last: Vessières

first: Scott

last: Hammack

first: Keiko

last: Nonomura

first: Julie

last: Favre

first: Linda

last: Grimaud

first: Matt

last: Petrus

first: Allain

last: Francisco

first: Jingyuan

first: Van

last: Lee

first: Fu-li

last: Xiang

first: James

middle: K

last: Mainquist

first: Stuart

middle: M

last: Cahalan

first: Anthony

last: Orth

first: Shang

last: Ma

first: Viktor

last: Lukacs

first: Laura

last: Bordone

first: Michael

last: Bandell

first: Bryan

last: Laffitte

first: Yan

first: Shu

last: Chien

first: Daniel

last: Henrion

first: Ardem

last: Patapoutian


title: Role of loss of Pofut1 expression on self-renewal and differentiation of adult neural progenitor cells

status: Public on Apr 16 2018

first: Paul

last: Martin

address: 700 Childrens Dr.

department: Center for Gene Therapy

institute: Nationwide Childrens Hospital

summary:
Reduced NotchR signaling has been implicated in the reduced division and differentiation of stem cells in a number of tissues.  The Protein-O-fucosyltransferase 1 gene (Pofut1) encodes a glycosyltransferase that O-fucosylates EGF-repeat-containing proteins, including Notch Receptors (NotchRs), and absence of Pofut1 glycosylation on NotchRs inhibits ligand-induced NotchR signaling.
Here, we have deleted Pofut1 in the brain by making NestinCrePofut1FF mice to investigate the role of loss of Pofut1 expression on self-renewal and differentiation of adult neural progenitor cells (ANPs).

overall_design: A total of six samples in three groups were analyzed for this study. The first group is two replicates of Nestin cre/Pofut1flox/flox brains. The second group is two replicates of Nestin cre/Pofut1 wild type brains. The third group is two replicates of Pofut1flox/flox brains.

first: Mi-Lyang

last: Kim


title: Mesenchymal TNFR2 promotes the development of polyarthritis and comorbid heart valve stenosis.

status: Public on Apr 23 2018

city: Vari

first: George

last: Kollias

address: 34 Fleming Street

department: Institute of Immunology/Department of Physiology, School of Medicine

institute: BSRC "Alexander Fleming"/National and Kapodistrian University of Athens

summary: This study demonstrates that arthritis and heart valve stenosis comorbidity, the most common condition among RA and SpA patients, share common mesenchymal requirements converging in the pathogenic activation of resident mesenchymal origin fibroblasts in the TnfARE mouse model. TNFR2 signaling, in this context, orchestrates the molecular mechanisms underlying arthritis and heart valve stenosis manifestation by regulating fibroblasts pathogenic activation status, cell proliferation and pro-inflammatory milieu. Finally this work highlights the complexity of TNFR2 functions since mesenchymal signaling is detrimental, whereas systemic TNFR2 provides protective signals that contain both pathologies

overall_design: 3’ RNA-Seq (QuantSeq) profiling of 2 cell types (SFs,VICs) in two different genotypes (TNF-DeltaARE, ColVIp75f/f-TNF-DeltaARE) and Wild type as control. 3 replicates per group.

first: Maria

last: Sakkou

first: Panagiotis

last: Chouvardas

first: Lydia

last: Ntari

first: Alejandro

last: Prados

first: Kristin

last: Moreth

first: Helmut

last: Fuchs

first: Valerie

last: Gailus-Durner

first: Martin

last: Hrabe de Angelis

middle: C

last: Denis

first: Niki

last: Karagianni


title: Identification of rapamycin as an autophagy inducer to treat PANC-1 cells

status: Public on Apr 17 2018

city: Nanning

first: Qiao

last: Yu

address: Shuangyong road, qingxiu district，nanning

institute: First Affiliated Hospital of Guangxi Medical University

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

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

overall_design: Refer to individual Series


title: Identification of rapamycin as an autophagy inducer to treat PANC-1 cells [mRNA, circRNA, lncRNA]

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

summary: The function and mechanism of autophagy in pancreatic cancer remained elusive owing to its complex biological process and multi-molecular involvement including non-coding RNAs. Here, we, from the view of mRNA, circRNA, lncRNA and miRNA, investigate the molecular mechanism of autophagy induction on human pancreatic cancer cells

overall_design: The autophagy-induced model was constructed with PANC-1 cells treated by rapamycin. It was indicated that 100µM rapamycin was the best choice to induce the autophagy of PANC-1 in humans.

first: Dan-ming

last: Wei

first: Rong-quan

last: He

first: Meng-tong

last: Jiang

first: Peng

last: Lin

first: Jie

last: Ma

first: Hong

last: Yang

first: Dian-zhong

last: Luo

first: Yi-wu

last: Dang

first: Gang

last: Chen


title: Immunomodulation with minocycline rescues retinal degeneration in juvenile neuronal ceroid lipofuscinosis (jNCL) mice highly susceptible to light damage

status: Public on Aug 17 2018

city: Cologne

first: Thomas

last: Langmann

address: Kerpener Strasse 62

department: Department of Ophthalmology

institute: University of Cologne

summary: We compared retinal transcriptomes of jNCL mice and wild-type mice under conditions of light damage

overall_design: total RNA from mouse retinas of Balb/c mice and jNCL mice under conditions of no light, high light, treatment with minocycline or solvent was analyzed using Affymetrix Clariom S (mouse) arrays. Biological duplicates were performed for each condition.

first: Katharina

last: Dannhausen


title: Maternal mRNA degradation by TUT4 and TUT7 in the zebrafish maternal-to-zygotic transition

status: Public on Apr 13 2018

city: Seoul

first: Hyeshik

last: Chang

state: South Korea

address: Building 203 Room 525, School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

institute: Seoul National University

summary: During the maternal-to-zygotic transition (MZT), maternal RNAs are actively degraded and replaced by newly-synthesized zygotic transcripts in a highly coordinated manner. However, it remains largely unknown how maternal mRNA decay is triggered in early vertebrate embryos. Here, through genome-wide profiling of RNA abundance and 3′ modification, we show that uridylation is induced at the onset of maternal mRNA clearance. The temporal control of uridylation is conserved in vertebrates. When the homologs of terminal uridylyltransferases TUT4 and TUT7 (TUT4/7) are depleted in zebrafish and Xenopus, maternal mRNA clearance is significantly delayed, leading to developmental defects during gastrulation. Short-tailed mRNAs are selectively uridylated by TUT4/7, with the highly uridylated transcripts degraded faster during the MZT than those with unmodified poly(A) tails. Our study demonstrates that uridylation plays a crucial role in timely mRNA degradation, thereby allowing the progression of early development.

overall_design: Examination of zebrafish embryos injected with control or TUT4/7 morpholinos at 1-cell stage. RNA-seq libraries were prepared at different time points across the MZT period. Three experimental sets, rs1a, rs2b, and rs2,  were conducted independently.

first: Jinah

last: Yeo

first: Jeong-gyun

last: Kim

first: Kyu-Won

first: V


title: Piwi knockdown in Drosophila Intestinal Stem Cells

status: Public on Apr 06 2018

city: Novato

first: Pedro

last: Sousa-Victor

state: CALIFORNIA

address: 8001 Redwood Blvd.

institute: Buck Institute for Research on Aging

summary: Transcriptome analysis of Piwi-deficient ISCs isolated by FACS. We used esg::Gal4, UAS::GFP; tub::Gal80ts to drive the expression of an RNAi against mCherry (control) or Piwi for 7 days.

overall_design: Duplicates of mCherry RNAi expressing ISCs and Piwi RNAi expressing ISCs. Each sample was obtained from a pool of 100 dissected and FACSorted fly guts.

first: Heinrich

last: Jasper


title: NOD2- and disease-specific gene expression profiles of peripheral blood mononuclear cells from Crohn’s disease patients

status: Public on Apr 03 2018

city: Rostock

first: Dirk

last: Koczan

address: Schillingallee 70

department: Institute for Immunology

institute: University of Rostock

summary: Employing microarray assays, a total of 267 genes were identified that were significantly  up- or downregulated in PBMCs of WT-NOD2 patients, compared to healthy donors  after challenge with vitamin D (+/-D) and/or a combination (+/-LP) of LPS (lipopolysaccharide) and PGN (peptidoglycan) (p < 0.05;  threshold: ≥ 2-fold change). For further analysis by real-time PCR, 12 genes with known  impact on inflammation and immunity were selected that fulfilled predefined  expression criteria. In a larger cohort of patients and controls, a disease-associated  expression pattern, with higher transcript levels in vitamin D-treated PBMCs from 5  patients, was observed for three of these genes, CLEC5A (p < 0.030), lysozyme (LYZ;  p < 0.047) and TREM1 (p < 0.023). Six genes were found to be expressed in a NOD2-  dependent manner (CD101, p < 0.002; CLEC5A, p < 0.020; CXCL5, p < 0.009; IL-24,  p < 0.044; ITGB2, p < 0.041; LYZ, p < 0.042). Interestingly, the highest transcript levels  were observed in patients with heterozygous NOD2 mutations.

overall_design: PBMC`s of 3 patient and 3 controls were treated with vitamin D and/or a combination of LPS and PGN resulting in 8 triplicates (24 hybridization samples)

first: Holger

last: Schäffler

first: Maria

last: Rohde

first: Sarah

first: Astrid

last: Huth

first: Nicole

last: Gittel

first: Hannes

last: Hollborn

first: Änne

last: Glass

first: Georg

last: Lamprecht

first: Robert

last: Jaster


title: Transcriptional profiling of C57BL-mice with humanized CAR/PXR or CAR/PXR-knockout treated with DCB and CPA

city: Basel

first: Jonathan

last: Moggs

address: Fabrikstrasse 2

institute: Novartis

summary: To investigate the role of the nuclear receptors CAR (constitutive androstane receptor) and PXR (Pregnane X receptor) in mediating the effects of non-genotoxic carcinogens, groups of mice humanised or deleted for CAR and PXR were treated with 1,4-Dichlorobenzene or cyproterone acetate for 3d and liver tissue harvested for expression profiling. Control groups were treated with appropriate vehicles.

overall_design: Group size was 5 mice (mus musculus, C57BL/6J, randomly assigned); all chemicals were of the highest quality available, and were administered by experienced personnel.

first: Colin

last: Henderson

first: Michael

last: Römer

first: Rita

last: Moreno

first: Lynsey

last: Chatham

first: Amy

last: Cameron

first: Jennifer

last: Grant

first: Roland

last: Wolf


title: Global gene expression profile of primary cultured keratinocytes with or without stimulation

first: Chen

last: Dong

address: Haidian District

department: Institute for Immunology and School of Medicine

institute: Tsinghua University

summary: Skin tissues from newborn C57BL/6 mice were obtained for primary keratinocyte culture. Cells were then stimulated with or without IL-25 (Biolegend) for 8hrs. Total RNAs were isolated with RNAprep pure Tissue Kit (DP431) and the RNA-seq library was prepared by the Beijing Genomics Institute. Sequence reads were obtained using BGIseq500 (Illumina) and successfully mapped to mouse genome. Reads counts were normalized based on RPKM, fold changes were calculated for all possible comparisons.

overall_design: Gene expression primary cultured keratinocytes with or without stimulation

first: Miao

last: Xu

first: Huiping

last: Lu

first: Xiaohong

last: Zhao


title: RNA-seq analysis of FACS-sorted control and Tsc2-deleted nociceptors

status: Public on Apr 01 2018

city: St Louis

first: Dan

last: Carlin

address: 660 S Euclid Ave / Campus Box 8108

department: Neuroscience

institute: Washington University in St Louis

summary: The goals of this study are to compare the transcriptomes of control heterozygous and Tuberous sclerosis 2 (Tsc2) homozygous nociceptors that have been enriched by fluorescence-associated cell sorting (FACS) with the aim of identifying differences in genes associated with sensory behavior. Nav1.8-Cre transgenic mice were used to delete Tsc2 as well as express Green fluorescent protein from the Rosa26 locus. Tsc2 deletion constitutively activates mTORC1 signaling cell autonomously. Dissociated dorsal root ganglia from adult mice were FACS-sorted for GFP and analyzed by RNA-seq. We find that a number of sensory behavior associated genes are affected by Tsc2 deletion including Calca, Ntrk1, Mrgpra3, and Nppb. Additionally, profiling of ion channel expression showed a reduction in almost half of expressed sodium, potassium and calcium channel as well as G-protein coupled receptors. Other categories of genes such as transcription factors and ligand-gated ion channels contained an even numbers of up- and downregulated genes with many that did not change as a result of Tsc2 deletion. In addition, expression of most marker genes enriched in Isolectin B4 (IB4) negative neurons were strongly reduced in Tsc2 mutant nociceptors, consistent with reduced sensitivity to heat, which is a modality related to these neurons. We conclude Tsc2 deletion and consequent mTORC1 activation alters gene expression of nociceptors resulting in altered sensory thresholds.

overall_design: L4 dorsal root ganglia contralateral to sciatic nerve crush were harvested 3 days post-injury from mice with Nav1.8-Cre mediated expression of GFP from Rosa26 locus as well as heterozgous (control) or homozygous (cKO) deletion of Tsc2 were FACS-sorted by GFP expression for 3 technical replicates of 100 cells each. RNA-seq data from 4 biological replicates was collected.

first: Judith

middle: P

last: Golden

first: Amit

last: Mogha

first: Vijay

last: Samineni

first: Kelly

last: Monk

last: Gereau IV

first: Valeria

last: Cavalli


title: Transcriptomics of Toxoplasma gondii enteroepithelial stages

status: Public on Mar 30 2018

city: Zurich

first: Chandra

last: Ramakrishnan

address: Winterthurerstrasse 266a

department: Institute of Parasitology

institute: University of Zurich

summary: Toxoplasma gondii is a zoonotic pathogen for which felids serve as definitive hosts. In cats, the parasite undergoes several rounds of asexual replication before entering the sexual cycle which gives rise to oocysts that are shed into the environment. These then sporulate and become infective to humans and live stock. To understand the genes involved in the parasite development in the felid host and identify potential intervention targets, we designed a transcriptomic approach to compare the cat intestinal stages with the well characterised tachyzoites that mediate acute infection and tissue cysts that are responsible for chronic infection. Cats were infected with T. gondii tissue cysts from mouse brain and sampled the intestinal stages at day 3, 5 and 7 post infection. As an input sample, we also collected tissue cysts from mouse brain as well as in vitro cultivated tachyzoites. Total RNA was extracted, enriched for mRNA and used for cDNA synthesis. RNA-Seq was then performed to describe the transcriptomic repertoire of each time point/life cycle stage.

overall_design:
RNA-Seq of cat enteroepithelial stages and cultivated tachyzoites of Toxoplasma gondii
NIH subcontract grant number: HHSN272200900038C

first: Christoph

last: Lippuner

first: Walter

middle: U

last: Basso

first: Robert

last: Walker

first: Hubert

last: Rehrauer

first: Nicholas

last: Smith

middle: E

last: Grigg

first: Peter

last: Deplazes

first: Adrian

last: Hehl


title: Expression data from human macrophages treate with miR-1246 mimic/inhibitor

status: Public on Mar 27 2018

first: Ana

middle: I

last: Robles

address: 37 Convent Dr 37/3060D

institute: National Cancer Institute/NIH

summary:
MiR-1246 was found to promote tumorigenesis and metastasis in sevearl cancer types. In the context of tumor microenvironment, tumor-associated macrophages are a central part typically correlated with poor prognosis.
We used microarray data to determine the gene expression profile in M2-like macrophages when treated with an overexpression of miR-1246 (conducted by miR-1246 mimic). As controls, we used either scambaled mimic control sequence, or a miR-1246 inhibitor.

overall_design: Monocytes were grown from the blood of healthy donor and matured to become m2-like macrophages for 10 days. Then, macrophges were transfected with either scrambledcontrol, miR1246 mimic or miR1246 inhibitor.RNA was extracted using the miRneasy micro kit. Two biological repeats were used.

first: Tomer

last: Cooks


title: Transcriptome analysis of WT and CD2AP KO TFH cells in LCMV-c13 infection

status: Public on Apr 09 2018

city: Saint Louis

first: Takeshi

last: Egawa

address: 660 South Euclid

department: Pathology and Immunology

institute: Washington University School of Medicine

summary: We report CD2AP KO TFH cells in LCMVc13 infection have enhanced cytokine production and cell cycling characteristics compared to WT cells

overall_design: Examination of RNA expression in TFH cells in WT and CD2AP KO cells

first: Saravanan

last: Raju


title: Effect of LSD1 knockdown on differentiating C2C12 myoblasts

status: Public on Mar 19 2018

city: Kumamoto

first: Kotaro

last: Anan

state: Kumamoto

address: 2-2-1, Honjo, Chuo-ku

department: Department of Medicall Cell Biology

institute: Kumamoto University

summary:
Analysis of differentiating LSD1-KD C2C12 myoblasts. We found LSD1 is an important regulator of oxidative phenotypes in skeletal muscle cells.
Results provide insight into the molecular mechanisms underlying roles of LSD1 in myocytes.

overall_design: C2C12 cells were transfected with SureSilencing Plasmids harboring shRNA against LSD1 (shLSD1, #336312 KM27305H, Qiagen) and non-targeting control (shControl, Qiagen #336312). Stable transfectants were selected in the presence of hygromycin. The selected C2C12 cells were induced to differentiate. 48 hours later total RNAs were isolated and subjected with microarray analysis.

first: Shinjiro

last: Hino

first: Mitsuyoshi

last: Nakao


title: Expression of FACS-sorted CD133+ and CD133- cells of three gastric cell lines

status: Public on Apr 04 2018

first: Tae-Min

last: Kim

address: Seocho-Gu, Banpo-Dong

department: Dept of Medical Informatics

institute: The Catholic University of Korea, College of Medicine

summary: To identify the gene expression signature associated with CD133, the well-known stem cell markers, three gastric cancer cell lines were obtained (KATO-III, SNU201 and SNU601). Cultured gastric cancer celllines were sorted into CD133+ and CD133- population by FACS sorting and microarray-based gene expression profiling was performed.

overall_design: Three GC celllines (KATO-III, SNU201 and SNU601) were purchased from the Korean Cell Line Bank and maintained in RPMI1640 medium supplemented with 10% calf serum. Cells were harvested and incubated in cell-staining buffer containing phycoerythrin (PE)-labeled anti-CD133/1(AC133) antibody. An isotype-matched PE-labeled control antibody was further employed to label the samples and set gating levels. The top 10% of CD133+ cells, in terms of fluorescence intensity, and the bottom 6% of CD133- cells, were collected via MoFlo XDP flow cytometry, which was also employed to sort cell lines into CD133+ and CD133- populations. Total RNA was isolated from sorted cells. The extracted RNA was further amplified and biotinylated using an Illumina TotalPrep RNA Amplification Kit. Extracted RNA was quantified on an Agilent 2100 Bioanalyzer. A Whole-Genome Expression Direct Hybridization Kit (Illumina) was used to hybridize 750 ng of cRNA from each sample to Human HT-12 v3 expression BeadChips (Illumina) at 58°C overnight. Unbound probe was removed by vigorous washing and the BeadChip was scanned with a BeadArray reader (Illumina).

first: Han

last: Lee


title: Expression data in MEFs

status: Public on Apr 05 2018

city: New York

first: Long

last: He

department: cancer center

institute: WCMC

summary: Determination of genes expression profile in MEFs with Foxk1 knock-down and add back

overall_design: MEFs established with Foxk1 shRNA and plus Foxk1 rescue,

first: John

last: Blenis

first: Xin

last: Wang


title: Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars

city: Berlin

first: Bastiaan

last: Spanjaard

address: Robert-Rössle-Straße 10

institute: Max Delbrück Center

summary: A key goal of developmental biology is to understand how a single cell transforms into a full-grown organism consisting of many different cell types. Single-cell RNA-sequencing (scRNA-seq) has become a widely-used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However, a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here, we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA-seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes, we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses, LINNAEUS (LINeage tracing by Nuclease-Activated Editing of Ubiquitous Sequences) can be used as a systematic approach for identifying the lineage origin of novel cell types, or of known cell types under different conditions.

overall_design: Combining scRNA-seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.

first: Bo

last: Hu

first: Nina

last: Mitic

first: Pedro

middle: O

last: Chauvet

first: Sharan

last: Janjuha

first: Nikolay

last: Ninov

first: Jan

last: Junker


title: Nuclear Receptor NR2F6 as an Alternative Cancer Immune Checkpoint in the T Cell Compartment

status: Public on Mar 14 2018

city: Innsbruck

first: Dietmar

last: Rieder

address: Innrain 80

department: Biocenter

institute: Medical University of Innsbruck

summary:
Analyzing mouse tumor models in vivo, human T cells ex vivo and human lung cancer samples, we provide direct evidence that NR2F6 acts as novel immune checkpoint. Genetic ablation of Nr2f6, particularly in combination with blockade of the established PD-L1 cancer immune checkpoint, efficiently delayed tumor progression and improved survival in experimental mouse models. The target genes deregulated in intratumoral T lymphocytes upon genetic ablation of Nr2f6 alone or together with PD-L1 blockade, revealed multiple advantageous transcriptional alterations for effective tumor rejection. In keeping with the above observation, acute Nr2f6 silencing in both mouse and human T cells induced hyper-responsiveness that established a non-redundant T cell-inhibitory function of NR2F6.
Analyzing mouse tumor models in vivo, human T cells ex vivo and human lung cancer samples,

overall_design: TILs derived from wild-type and Nr2f6-/- tumor-bearing mice collected at d14 after B16-OVA tumor cell injection. and subjected to detailed analysis, including FACS sequencing and RNA sequencing

first: Victoria

last: Klepsch

first: Natascha

last: Hermann-Kleiter

first: Patricia

last: Do-Dinh

first: Bojana

last: Jakic

first: Anne

last: Offermann

first: Mirjana

last: Efremova

first: Sieghart

last: Sopper

last: Krogsdam

first: Gabriele

last: Gamerith

first: Sven

last: Perner

first: Alexandar

last: Tzankov

first: Zlatko

last: Trajanoski

first: Dominik

last: Wolf

first: Gottfried

last: Baier


title: TP53INP2 knockdown in 3T3-L1 preadipocytes

city: Sabadell

first: Antoni

last: Berenguer-LLergo

state: Barcelona

address: Parc del Taulí, 1

department: A8G2 Group - Rheumatology Service

institute: Parc Taulí Research and Innovation Institute (I3PT)

summary: Excessive fat accumulation is a major risk factor for the development of type 2 diabetes.To determine the mechanisms by wich TP53INP2 regulates adipogenesis, gene expression profile was performed in TP53INP2-deficient 3T3-L1 cells at different stages of differentiation.

overall_design: TP53INP2-deficient 3T3-L1 cells, and their respective controls, at day 0 and 7 of differentiation were used in this study.

first: Antonio

last: Zorzano

first: Victor

last: Francis

first: Montserrat

last: Romero


title: RNA seq analysis on zebrafish Notch 3 mutants and adult neural stem cells

city: Rijeka

first: Tihana

last: Lenac Rovis

address: B. Branchetta 20

department: Center for Proteomics

country: Croatia

institute: University of Rijeka Faculty of Medicine

summary: The goal of this study is to identify the Notch3 targets directly responsible for maintaining the quiescent state and the stemness of adult pallial zebrafish Radial Glia.

overall_design: Three independent experiments with 15 larval brains for each condition were performed for library construction from genotyped notch3-/- mutant versus notch3+/+ larvae, crossed into the gfap:gf. Three independent experiments with 20 adult telencephali were performed for library construction from her4:drfp;mcm5:gfp double transgenic fish.

first: Emmanuel

last: Than-Trong

first: Alessandro

last: Alunni

first: Sébastien

last: Mella

first: Chirag

last: Nepal

first: Sara

last: Ortica


title: Expression data of colonic epithelial cells colonized with B. theta

status: Public on Apr 02 2018

city: Yokohama

first: Keiichiro

last: Suzuki

state: Kanagawa

address: 1-7-22 Suehiro-cho. Tsurumi

department: IMS

institute: RIKEN

summary:
The gut microbiota is essential for several aspects of host physiology such as metabolism, epithelial barrier function and immunity. Previous studies have revealed that host immune system as well as diet and other environmental factors have a strong impact on the composition and activity of gut microbiota, but the molecular requirements for such functional regulation remain unknown. We show that the bacteria belonging to phylum Bacteroidetes acquire their symbiotic activity in the colonic mucus, depending on a newly characterized molecular family encoded within the polysaccharide utilization loci (PUL), which we have named Mucus-Associated Functional Factor (MAFF).
We used microarray analysis of colonic epithlial cells to determin the impact of MAFF genes on colonic homeostasis.

overall_design: Specific pathogen free mice were treated with antibiotics (metronidazone and ciprofloxacin) and then colonized wild type or MAFF-deleted mutant of B. theta. Colonic epithelial cells were FACS-purified 4-weeks after colonization, and RNA samples were prepared.

first: Akira

last: Nakajima


title: Oncogenic RAS blocks myogenic differentiation

city: Bethesda

first: Javed

last: Khan

state: MD

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

summary: C2C12 mouse myoblasts expressing RAS mutants identified in human tumors fail to differentiate in low serum media.

overall_design: Microarray in C2C12 cell lines stably expressing empty vector (pBABE) or RAS mutants

first: Berkley

last: Gryder

first: Marielle

last: Yohe

first: Xinyu

last: Wen


title: Gfi1b - A key player in genesis and maintenance of AML and MDS [expression microarray]

status: Public on Mar 31 2018

city: Essen

first: Cyrus

last: Khandanpour

state: NRW

address: Hufelandstr. 55

department: Department of Hematology

institute: University Hospital Of Essen

summary:
Differentiation of hematopoietic stem cells (HSCs) is regulated by a concert of different transcription factors (TFs). A disturbed function of TFs can be the basis of (pre)malignancies such as myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML). Growth Factor Independence 1b (Gfi1b) is a repressing TF with a key role in quiescence of HSCs and emergence and maturation of erythrocytes and platelets. Here, we show that low expression of GFI1B in blast cells is associated with inferior prognosis of MDS and AML patients. Using mouse models with either reduced expression or conditional deletion of Gfi1b, crossed with a mouse model reflecting human MDS or AML, we demonstrate that AML development was accelerated with heterozygous loss of Gfi1b, and latency was further decreased when Gfi1b was conditionally deleted. Loss of Gfi1b significantly enhanced stemness of leukemic cells with upregulation of genes fundamentally involved in leukemia development. On a molecular level, we found that loss of Gfi1b not only increased the levels of reactive oxygen species (ROS) but also induced gene expression changes of key AML pathways such as the p38/AKT pathway. These results demonstrate that Gfi1b functions as an oncosuppressor in MDS/AML development.
We used microarrays to detail the effect of loss of Gfi1b expression on key AML-pathways in a mouse model system

overall_design: For bone marrow cells, femur, tibia and humerus were extracted from leukemic NUP98/HOXD13 mice. RNA was isolated from 5 x 10^6 – 1 x 10^7 bone marrow cells using the RNeasy Mini Kit.

first: Aniththa

last: Thivakaran

first: Lacra

last: Botezatu

first: Judith

last: Hönes

last: Schütte

first: Lothar

last: Vassen

first: Nadine

last: Olberding

first: Yahya

last: Al-Matary

first: Renata

last: Köster

first: Klaus

last: Lennartz

first: Andre

last: Görgens

first: Bernd

last: Giebel

first: Bertram

last: Opalka

first: Ulrich

last: Dührsen


title: Tipifarnib inhibits HRAS-driven dedifferentiated thyroid cancers: Adaptive responses and acquired mutations in Nf1 and Gnas are dirivers of resistance

first: Brian

middle: Roy

last: Untch

state: NY

address: 1275 York Ave

department: Surgery

institute: Memorial Sloan Kettering Cancer Center

summary: Affymetric arrays were performed on thyroid samples collected from GEMMs: Cre-negative, Tpo-cre;HrasG12V (Homozygous), Tpo-cre;HrasG12V,p53f/f (PDTC), Tpo-cre;HrasG12V,p53f/f (ATC)

overall_design: Thyroids and tumor-bearing thyroid glands were isolated from various mouse models at baseline

first: James

last: Fagin


title: Prenatal selective serotonin reuptake inhibitor (SSRI) exposure induces working memory and social recognition deficits by disrupting inhibitory synaptic networks in male mice

status: Public on Mar 07 2018

city: Ulsan

first: Taejoon

last: Kwon

address: 50 Unist-gil

department: Department of Biomedical Engineering

institute: Ulsan National Institute of Science and Technology

summary: Selective serotonin reuptake inhibitors (SSRIs) are commonly prescribed antidepressant drugs in pregnant women.  Given that SSRIs can cross the placental and blood-brain barriers, these drugs potentially affect serotonergic neurotransmission and neurodevelopment in the fetus.  Although no gross SSRI-related teratogenic effect has been reported, infants born following prenatal exposure to SSRIs have a higher risk for various behavioral abnormalities.  Therefore, we examined the effects of prenatal fluoxetine, the most commonly prescribed SSRI, on social and cognitive behavior in mice.  Intriguingly, chronic in utero fluoxetine treatment impaired working memory and social novelty recognition in adult males with augmented spontaneous inhibitory synaptic transmission onto the layer 5 pyramidal neurons in the medial prefrontal cortex (mPFC).  Moreover, fast-spiking interneurons in the layer 5 mPFC exhibited enhanced basal intrinsic excitability, augmented serotonin-induced neuronal excitability, and increased inhibitory synaptic transmission onto the layer 5 pyramidal neurons due to augmented 5-HT2A receptor (5-HT2AR) signaling.  More importantly, the observed behavioral deficits of in utero fluoxetine-treated mice could be reversed by acute systemic application of 5-HT2AR antagonist.  Taken together, our findings support the notion that alterations in serotonin-mediated inhibitory neuronal modulation result in reduced cortical network activities and cognitive impairment following prenatal exposure to SSRIs.

overall_design: We examined biological duplicate samples for each group.

first: Weonjin

last: Yu

first: Yi-Chun

last: Yen

first: Young-Hwan

last: Lee

first: Shawn

last: Tan

first: Yixin

last: Xiao

first: Hidayat

last: Lokman

first: Audrey

last: Ting

first: Hasini

last: Ganegala

first: Won-Kyung

last: Ho

first: H.

middle: S

last: Je


title: Microarray analysis comparing gene expression of callus tissue extracted from either Cyp24a1-null mice or their control heterozygous littermates

status: Public on Mar 29 2018

city: Montreal

first: Corine

last: Martineau

state: Quebec

address: 1003 Decarie Boulevard

department: Research Centre

country: Canada

institute: Shriners Hospital for Children - Canada

summary: The 24R,25-dihydroxyvitamin D metabolite (24R,25D) has long been suspected of participating to bone fracture repair. We used Cyp24a1-deficient mice, unable to produce 24R25D, to observe gene expression in callus tissue compared to that of control littermates.

overall_design: In total 6 samples; 3 from Cyp24a1-null mice with the corresponding control littermate samples

first: Roy

last: l Naja

first: René

last: St-Arnaud


title: Choline Kinase Alpha (CHKα) as a Therapeutic Target in Pancreatic Ductal Adenocarcinoma: Expression, Predictive Value, and Sensitivity to Inhibitors

status: Public on Mar 28 2018

city: Madrid

first: Enrique

last: Carrillo de Santa Pau

address: C/ Melchor Fernández Almagro, 3

department: Cancer Cell Biology Programme

institute: Spanish National Cancer Research Centre (CNIO)

summary: Choline kinase α (CHKα) plays a crucial role in the regulation of membrane phospholipid synthesis and has oncogenic properties in vitro. We have analyzed the expression of CHKα in cell lines derived from pancreatic ductal adenocarcinoma (PDAC) and have found increased CHKα expression, associated with differentiation. CHKα protein expression was directly correlated with sensitivity to MN58b, a CHKα inhibitor that reduced cell growth through the induction of apoptosis. Accordingly, CHKα knockdown led to reduced drug sensitivity. In addition, we found that gemcitabine-resistant PDAC cells displayed enhanced sensitivity to CHKα inhibition and, in vitro, MN58b had additive or synergistic effects with gemcitabine, 5-fluorouracil, and oxaliplatin, three active drugs in the treatment of PDAC. Using tissue microarrays, CHKα was found to be overexpressed in 90% of pancreatic tumors. While cytoplasmic CHKα did not relate to survival, nuclear CHKα distribution was observed in 43% of samples and was associated with longer survival, especially among patients with well/moderately differentiated tumors. To identify the mechanisms involved in resistance to CHKα inhibitors, we cultured IMIM-PC-2 cells with increasingly higher concentrations of MN58b and isolated a subline with a 30-fold higher IC50. RNA-Seq analysis identified upregulation of ABCB1 and ABCB4 multidrug resistance transporters, and functional studies confirmed that their upregulation is the main mechanism involved in resistance. Overall, our findings support the notion that CHKα inhibition merits further attention as a therapeutic option in patients with PDAC and that expression levels may predict response.

overall_design: RNAseq from parental (IMIM-PC2 cell line)) and MN58b-resistant cells by triplicate

first: Jose

last: Mazarico

first: Víctor

middle: J

last: Sánchez Arévalo-Lobo

first: Francisco

middle: X

last: Real


title: RNA-seq of bone marrow derived macrophages stimulated with monophosphoryl lipid A (MPLA)

city: Nashville

first: Benjamin

middle: Ari

last: Fensterheim

state: TN

address: 1161 21st Avenue South

department: Pathology, Microbiology, and Immunology

institute: Vanderbilt University

summary: We found that MPLA reprograms macrophages in a way that supports a persistent monocyte/macrophage chemokine secretion profile reflected in macrophage mRNA. Additionally, this RNA-seq data revealed that certain genes (e.g. phagocytosis-related) persist much longer after MPLA than others (e.g. pro-inflammatory cytokines).

overall_design: Bone marrow derived macrophages were harvested for RNA after 4hrs of monophosphoryl lipid A (MPLA) priming, 24hrs of MPLA priming, and 3 days following the end of priming

middle: A

first: Julia

last: Bohannon


title: Gene expression in the liver remnant is significantly affected by the size of partial hepatectomy - an experimental rat study

city: Aarhus C

first: Anders

middle: Riegels

last: Knudsen

address: Nørrebrogade 44, building 1c, LVN-research

department: Department of Surgery, Section for upper GI surgery

country: Denmark

institute: Aarhus University Hospital

summary:
Background: Extended hepatectomies may result in post-hepatectomy liver failure, a condition with a high mortality. The main purpose of the present study was to investigate and compare the gene expression profiles in rats subjected to increasing size of partial hepatectomy.
Methods: 40 Wistar rats were subjected to 30%, 70%, or 90% partial hepatectomy, sham operation or no operation. 24 hours following resection, liver tissue was harvested and genome-wide expression analysis was performed.
Results: Cluster analysis revealed 2 main groupings, one containing the PH(90%) and one containing the remaining groups (baseline, sham, PH(30%) and PH(70%)). Categorization of specific affected molecular pathways in the PH(90%) group revealed a downregulation of cellular homeostatic functions degradation and biosynthesis, whereas proliferation, cell growth, and cellular stress and injury were upregulated in the PH(90%) group. After PH(90%), the main upregulated pathways were mTOR and ILK. The main activated upstream regulators were hepatocyte growth factor and transforming growth factor.
Conclusion: With decreasing size of the future liver remnant, the liver tended to prioritize expression of genes involved in cell proliferation and differentiation at the expense of genes involved in metabolism and body homeostasis. This prioritizing may be an essential molecular explanation for post-hepatectomy liver failure.

overall_design: Rats were subjected to different size hepatectomi. 30 rats were randomly subjected to either 30%, 70%, 90%, Sham or Control operation. The rats were put down 24 hours after the operation, the liver removed and biopsies for gene expression analysis were harvested.


title: ATAC-Seq analysis in vasopressin-responsive mouse renal collecting duct mpkCCD cells

status: Public on Mar 26 2018

city: Baltimore

first: Hyun Jun

last: Jung

address: 720 Rutland Ave, Ross Research Building 1165B

department: Medicine (Nephrology)

institute: Johns Hopkins University School of Medicine

summary: Vasopressin, a peptide hormone, controls renal water excretion, largely through regulation of water channel aquaporin-2 (AQP2) in the renal collecting duct. There are two regulatory mechanisms of AQP2: 1) short-term regulation by membrane trafficking of AQP2; and 2) long-term regulation involving vasopressin-induced changes of protein abundance of AQP2 through regulation of gene transcription and protein half-life. Vasopressin binds a G protein-coupled receptor (V2R) activating several downstream signaling pathways. At downstream of V2R activation, many of transcription factors involve gene transcription process associated with status of chromatin structure. ATAC-Seq (Assay for Transpoase-Accessible Chromatin using Sequencing) is a recent technique to study chromatin accessibility (Buenrostro et al. Nat Methods 2013). We carried out ATAC-Seq following standard an ATAC-Seq protocol in mpkCCD cells treated with vehicle or dDAVP for 30 minutes.

overall_design: To identify Tn5-accessible chromatin regions where transcription factors may bind, we carried out ATAC-seq . Observations were made both after 30 minutes treatment with the vasopressin analog dDAVP or vehicle (n=2 for each group).

first: Mark

last: Knepper


title: Effect of LSD1 inhibition on differentiating C2C12 myoblasts

first: Kotaro

last: Anan

institute: Kumamoto University

summary: Analysis of differentiating C2C12 myoblasts treated with two LSD1 specific inhibitors. We found LSD1 is an important regulator of oxidative phenotypes in skeletal muscle cells.  Results provide insight into the molecular mechanisms underlying roles of LSD1 in myocytes.

overall_design: C2C12 cells were induced to differentiate with LSD1 inhibitors, tranylcypromine (TC) or S2101, or vehicle control. 48 hours later total RNAs were isolated and subjected with microarray analysis.

first: Shinjiro

last: Hino

first: Mitsuyoshi

last: Nakao


title: Splicing events and transcriptome changes upon TDP-43 and FUS knock-down in human neuroblastoma cells

status: Public on Mar 18 2018

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

summary: We performed exon array analysis to define and compare the transcriptomic changes, in terms of splicing and gene expression profilings, occurring in human neuroblastoma cells upon knocking down TDP-43 and FUS RNA-binding proteins (RBP), with the final aim to unravel the biological role of these RBPs in neuronal cells.

overall_design: To identify the differentially expressed and spliced genes, the microarray-based technology was performed using the recovered total RNAs from triplicate experimental knocked-down samples (siTDP-43 samples, siFUS samples and the control mock siCTRL samples).

first: Antonia

last: Ratti


title: Expression data of E7.5 primary germ layers [microarray]

status: Public on Mar 17 2018

city: Jinan

first: Xukun

last: Lu

address: No. 44 Wenhua West Road

institute: Shandong University

summary:
Alternative splicing (AS) and alternative promoter (AP) usage expand the repertories of mammalian transcriptome profiles and thus diversify gene functions. However, our knowledge about the extent and functions of AS and AP usage in mouse early embryogenesis remains elusive. Here, by performing whole-transcriptome splicing profiling with high-throughput next generation sequencing, we report that AS extensively occurs in embryonic day (E) 7.5 mouse primary germ layers, and may be involved in multiple developmental processes. In addition, numerous RNA splicing factors are differentially expressed and alternatively spliced across the three germ layers, implying the potential importance of AS machinery in shaping early embryogenesis. Notably, AP usage is remarkably frequent at this stage, accounting for more than one quarter (430/1648) of the total significantly different AS events. Genes generating the 430 AP events participate in numerous biological processes, and include important regulators essential for mouse early embryogenesis, suggesting that AP usage is widely used and might be relevant to mouse germ layer specification. Our data underline the potential significance of AP usage in mouse gastrulation, providing a rich data source and opening another dimension for understanding the regulatory mechanisms of mammalian early development.
The Microarray was used to measure gene expression in E7.5 mouse primary germ layers, which was compared to an independent RNA-seq data performed in our lab.

overall_design: The gene expression patterns were obtained using Microarray and compared between different germ layers.

first: Lei

last: Li


title: Gene expression in Mist1+ cells

city: Tokyo

first: Yoku

last: Hayakawa

state: TOKYO

address: 7-3-1, Hongo, Bunkyo-ku, Clinical Research Center 4F, Room 425

institute: University of Tokyo

summary:
Mist1+CD24hi cells and Mist1+CD24lo cells in mouse small intestine were separatedly sorted, and RNAs were isolated.
Mice were treated with irradiation, Lgr5-DT ablation, doxorubicin, or NICD expression before sorting.

overall_design: TdTomato+ cells were gated by CD24 and sorted by FACS. Each group has 2 replicates. Groups contain untreated control, irradiated, Lgr5-ablated, doxorubucin-treated, and NICD-expressed samples.

first: Samuel

last: Asfaha

first: Hiroto

last: Kinoshita

first: Mitsuru

last: Konishi

first: Masahiro

last: Hata

first: Mayo

last: Tsuboi

first: Woosook

last: Kim

first: Moritz

last: Middelhoff

first: Yohko

last: Hikiba

first: Sozaburo

last: Ihara

first: Tetsuo

last: Ushiku

first: Masashi

last: Fukayama

first: Yagnesh

last: Tailor

first: Yoshihiro

last: Hirata

first: Chandan

last: Guha

first: Kelley

last: Yan

first: Kazuhiko

last: Koike

first: Timothy

last: Wang


title: HDAC1/2 are required for microglia identity during development, homeostasis and neurodegeneration in a context-dependent manner [ChIP inducible knockout on FAD background]

city: Freiburg

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

institute: University Medical Center Freiburg

summary: Microglia as tissue macrophages of the central nervous system (CNS) provide immunological defense and contribute to the establishment and maintenance of CNS homeostasis. Several transcription factors have been described that regulate microglia development and its steady state form, however little is known about the epigenetic signals that control microglia function in vivo. Here, we employed constitutive and inducible mutagenesis in microglia to delete two class I histone deacetylases (HDACs), Hdac1 and 2. Prenatal ablation of Hdac1 and 2 from microglia drastically impaired microglial development with reduced cell number, altered morphology and induction of apoptosis. Comparative transcriptomic profiling revealed an essential role of Hdac1/2 in the regulation of microglia survival and expansion. Mechanistically, hyperacetylation at H3K9 and H3K27 was found at the promoters of pro-apoptotic and cell cycle genes in the absence of Hdac1/2. In contrast, Hdac1/2 were not required in adult microglia during homeostasis. In a mouse model of Alzheimer’s disease, suppression of Hdac1/2 in microglia, but not in neuroectodermal cells, remarkably displayed substantial decrease in amyloid load and improved cognitive impairment by enhancing microglial amyloid phagocytosis. Collectively, we report a previously unknown role of epigenetic factors that differentially affect microglia development, homeostasis and disease that could potentially be utilized therapeutically.

overall_design: HDAC1/2-2lox-Cx3cr1-CreERT2 microglia from aged mice on the 5xFAD background were sorted and ChIP was performed for histone marks H3K9ac and H3K27ac. Samples were compared to Cre negative FAD positive controls using 2 or 3 replicates.

first: Moumita

last: Datta

first: Elena

last: Raschi

first: Maximilian

last: Frosch

first: Nora

last: Hagemeyer

first: Tuan

middle: L

last: Tay

first: Thomas

last: Blank

first: Melanie

last: Meyer-Luehmann

first: Marco

last: Prinz