title: Light-dependent expression profiles in WT, DKO, and TKO zebrafish

status: Public on Feb 27 2019

city: Tokyo

first: Jun

last: Hirayama

address: 1-5-45 Yushima, Bunkyo-ku

department: Medical Research Institute

country: Japan

institute: Tokyo Medical and Dental University

summary: To identify the underlying mechanism causing the defects in light-dependent behavioral rhythm formation  and the reduced locomotor activity in DKO and TKO zebrafish, a microarray analysis was conducted.

overall_design: We prepared nine samples from WT, DKO, or TKO zebrafish treated with 3-h light, 12-h light, and those kept in darkness.

first: Hiroshi

last: Nishina


title: Gene expression profiles of Ecrg4-wt, -hetero and -homo NSCs

city: Sapporo

first: Toru

last: Kondo

address: Kita-15, Nishi-7, Kita-ku,

department: Institute for Genetic Medicine

institute: Hokkaido University

summary: To identify factors that increase and decrease in Ecrg4 deficient NSCs


title: AMPK inhibitors may be potential drugs for STING-induced inflammatory diseases.

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

country: USA

institute: University of Miami

summary: AMPK inhibitors suppress inflammatory gene expression induced by STING R284S variants.

overall_design: STING R284S variant was expressed in STING-/- MEF cells. RNA was extracted from the MEF cells after treated with AMPK inhibitors and Affymetrix microarray was used to analyze gene expression in the MEF cells.

first: Hiroyasu

last: Konno


title: Helicase subunit Cdc45 targets the checkpoint kinase Rad53 to both replication initiation and elongation complexes after fork stalling

status: Public on Feb 26 2019

city: Cambridge

first: Charles

last: Bradshaw

address: Tennis Court Road

department: Gurdon Institute

country: United Kingdom

institute: University of Cambridge

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Across eukaryotes, inhibition of the progression of the DNA replication machinery causes an S-phase checkpoint response. This response regulates multiple processes, including inhibition of replication initiation and fork stabilisation. How these events are coordinated remains poorly understood. Here we show that the replicative helicase component Cdc45 targets the checkpoint kinase Rad53 to distinct replication complexes in the budding yeast Saccharomyces cerevisiae. Rad53 binds to FHA-interaction motifs in an unstructured loop region of Cdc45, which is phosphorylated by Rad53 itself, and this interaction is necessary for the inhibition of origin firing through Sld3. In addition to regulating replication initiation, Cdc45 also recruits Rad53 to stalled replication forks, which we demonstrate is important for the response to replication stress. Finally we show that a Cdc45 mutation that is orthologous to an allele found in patients with Meier-Gorlin Syndrome disrupts the functional interaction with Rad53. Together we present a single mechanism by which Rad53 targets replication initiation and elongation complexes, which may be relevant to human disease.

overall_design: Reads were mapped to W303 genome. All the normalisation and data processing steps done by used Deeptools. ChIP data was analysed by normalising the read counts to +/-500bp of centromeric reads. For visualization, centromeric regions were masked out.  For replication profiles, a dormant replicative region was defined as the 10 kb region between two late/dormant origins of maximal base pair distance. It was assumed that there was no replication in such regions after 1h HU treatment. 10 such origin pairs were chosen as the dormant region set. Replication profiles were obtained using the following methodology:  1) S-phase samples were normalized to G1 samples by binning each chromosomal region to 100bps and dividing the G1 sample counts over the S-phase samples counts.  2) The average count of the dormant region set from all samples was taken as 1N.  3) The relative count of all regions in 100bp bins was calculated as a ratio of 1N.   4) Relative ratios bigger than 2.2N were masked out.

first: Geylani

last: Can

first: Philip

last: Zegerman


title: Expression profiles of Ecrg4hetero beta-gal positive neurosphere and Ecrg4hetero beta-gal positive VZ/SVZ

summary: To find factors that increase and decrease in VZ/SVZ

overall_design: We found that Ecrg4 negatively regulates NSC proliferation in vivo.


title: Transcriptome analysis of EDS1-R493A after Pst AvrRps4- triggered immunity

city: Cologne

first: Deepak

middle: Dharamchand

last: Bhandari

email: bhandari@mpipz.mpg.de, dharamch@msu.edu

state: nrw

address: Carl-von-linne-weg, 10

department: Plant-Microbe interactions

country: Germany

institute: Employer

type: Expression profiling by high throughput sequencing

summary: We present here the transcriptominc changes occuring after TNL-triggered immunity after infection with pst AvrRps4 in a point mutant of EDS1, EDS1-R493A

overall_design: mRNA transcripts of Col-0, eds1-2, cEDS1(wt) and EDS1-R493A at 0 (untreated), 8 and 24 hpi with pst AvrRps4 and pst ΔCOR AvrRps4 were deep sequenced, in triplicates using illumina. 4 week old plant leaves were syringe infiltrated at a concentration of 0.005

first: Jane

middle: E

last: Parker

middle: D


title: Homo sapiens whole genome expression microarray of endometrium obtained from fertile and Infertile women with stage IV ovarian endometriosis and without endometriosis

city: Delhi

first: Muzaffer

middle: Ahmed

last: Bhat

state: Delhi

address: ANSARI NAGAR NEW DELHI 110029

department: Physiology

country: India

institute: AIIMS

summary:
The hypothesis that male michrochimerism in eutopic endometrium is a factor for endometriosis, as indicated by indirect evidence was examined in endometrial samples from control (Group 1) and stage IV ovarian endometriosis (Group 2), either fertile (Group 1A and 2A) or Infertile (Group 1B and 2B) pateints.
6 coding and 10 non-coding genes showed bi-modal pattern of expression characterised by low expression in samples obtained from fertile patients and high expressions in infertile patients. Several coding and non-coding MSY-linked genes displayed michrochimerism in form of presence of their respective DNA inserts along with their microarray-detectable expression in endometrium irrespective of fertility history and disease.

overall_design: Whole genome expression arrays of endometrial total RNA obtained from  endometrium of women without endometriosis (Group 1) and with stage IV ovarian endometriosis (Group 2), either fertile (Group 1A and 2A) or Infertile (Group 1B and 2B).

middle: A

first: Debabrata

last: Ghosh


title: Identification of a NAC Transcription Factor for the Elicitation of Glyceollin Biosynthesis in Soybean Reveals a Conserved Phytoalexin Regulatory Pathway

city: Morgantown

first: Nik

last: Kovinich

state: WV

address: 1194 Evansdale Drive

department: Plant and Soil Sciences

institute: West Virginia University

summary: Glyceollins are inducible defense metabolites (phytoalexins) that belong to the isoflavonoid family of molecules that are biosynthesized in soybean in response to pathogens and some abiotic stresses.

overall_design: Glyceollin metabolite accumulation was elicited in Harosoy63 soybean seedlings that were transferred to germination paper saturated with pH 3.0 medium compared to paper saturated with pH 5.8  medium (control) at 9 days after transfer, whereas seedlings transferred to germination paper that was saturated with pH 5.8 medium then allowed to dry for 6 days (dehydration treatment) had reduced glyceollin metabolite levels compared to the control pH 5.8 filter paper that was continuously saturated with medium (not allowed to dry). Media was half-strength Murashige and Skoog (MS) salts, 1% sucrose, with MS vitamins.


title: Pro-Inflammation Associated with a Gain-of-Function Mutation (R284S) in the Innate Immune Sensor STING

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

overall_design: Refer to individual Series


title: The differential expression of microRNA in human normal colorectal mucosa cells and human colon cancer cells

city: Guangzhou，China

first: jide

last: Wang

state: Guangdong ，China

address: 1838 Guangzhou Avenue North

department: Department of Digestive Medicine

country: China

institute: Nanfang Hospital, Southern Medical University

summary: Microarrays were used to screen differentially expressed microRNAs in FHC and SW620 LoVo cells.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: In the experiments, we used the chip to detect the probe signal values of FHC, SW620 and LoVo cells, set 3 replicates per cell line, and then used FHC as a control to screen for microRNAs that were up- or down-regulated simultaneously in SW620 and LoVo cells.

first: Jide


title: Differential gene expression differences between tolerant and susceptible avocado rootstocks in response to Rosellinia necatrix infection

city: Pretoria

first: Dave

middle: Kenneth

last: Berger

state: Gauteng

address: Lynnwood Road

department: Plant and Soil Science

country: South Africa

institute: University of Pretoria

summary: Background: Rosellinia necatrix is the causal agent of avocado white root rot (WRR). Control of this soil-borne disease is difficult and tolerant rootstocks may represent an effective method to lessen its impact. To date, no studies on molecular mechanisms regulating the avocado plant response towards this pathogen have been undertaken. To shed light onto the mechanisms underpinning disease susceptibility and tolerance, molecular analysis of the gene's response of two contrasting-disease-reaction avocado rootstocks was assessed.  Results: Gene expression profiles against R. necatrix were assessed in the susceptible 'Dusa' and the tolerant selection BG83 avocado genotypes by micro-array analysis. In 'Dusa', the early response is mainly related to redox processes and cell-wall degradation activities, all becoming more remarkable after disease progression affected photosynthetic capacity; whereas, tolerance to R. necatrix in BG83 relies on the induction of protease inhibitors and their negative regulators, as well as salt and osmotic stress related genes besides oxido-reduction processes. We identified three protease inhibitors, glu protease, trypsin and endopeptidase inhibitors, highly overexpressed in the tolerant genotype, when compared to susceptible 'Dusa', after infection with R. necatrix, reaching fold change values of 44, 34 and 16 respectively.  Conclusions: The contrasting results between 'Dusa' and BG83 give new insights into the different mechanisms involved in the avocado tolerance to P. cinnamomi and R. necatrix, which are consistent with their biotrophic and necrotrophic lifestyles, respectively. The differential induction of genes involved in salt and osmotic stress in BG83 could indicate that R. necatrix penetration into the roots is associated with osmotic effects suggesting that BG83's tolerance to R. necatrix is related to the ability to withstand osmotic imbalance. In addition, the high expression of protease inhibitors in tolerant BG83 compared to susceptible 'Dusa' after infection with the pathogen, suggests the important role that these proteins could play in the defence of avocado rootstocks against R. necatrix.

overall_design: Direct comparison, three biological replicates control vs infected for Dusa strains, two biological replicates control vs infected for BG83 strain

first: A

last: Zumaquero

first: E

last: Martínez-Ferri

middle: J

last: Matas

first: B

last: Farrow

first: N

last: Olivier

first: F

last: Pliego-Alfaro

last: Barceló

last: van den Berg

first: C

last: Pliego


title: Stress-induced inactivation of the Staphylococcus aureus purine biosynthesis repressor leads to  hypervirulence

city: London

first: Mariya

last: Goncheva

state: Ontario

address: Dental Services Building Room 3014, 1151 Richmond Street

department: Microbiology and Immunology

country: Canada

institute: The University of Western Ontario

summary: Staphylococcus aureus is a significant cause of human infection. Here, we demonstrate that mutations in the transcriptional repressor of purine biosynthesis, purR, enhance the pathogenic potential of S. aureus. Indeed, systemic infection with purR mutants causes accelerated mortality in mice, which is due to aberrant up-regulation of fibronectin binding proteins (FnBPs). Remarkably, purR mutations can arise upon exposure of S. aureus to stress, such as an intact immune system. In humans, naturally occurring anti-FnBP antibodies exist that, while not protective against recurrent S. aureus infection, ostensibly protect against hypervirulent S. aureus infections. Vaccination studies support this notion, where anti-Fnb antibodies in mice protect against purR hypervirulence. These findings provide a novel link between purine metabolism and virulence in S. aureus.

overall_design: 3 biological replicates of both the WT and the mutant were analysed

first: David

last: Heinrichs


title: Transcriptome analysis of Escherichia coli strains producing exogenous internal membrane proteins

city: Rosario

first: Pablo

middle: Emiliano

last: Tomatis

address: Ocampo y Esmeralda

country: Argentina

institute: IBR-CONICET

overall_design: 6 samples, 3 replicates

first: Andreas

last: Plueckthun


title: Requirements for preinitiation complex formation in vivo

city: Boston

first: Natalia

last: Petrenko

state: MA

address: 240 Longwood Ave

department: BCMP

institute: Harvard Medical School

summary: Transcription by RNA polymerase (Pol) II requires assembly of a preinitiation complex (PIC) composed of general transcription factors (GTFs) bound at the core promoter.  In vitro, the TATA-binding protein (TBP), TFIIB, TFIIF, and Pol II are essential for PIC formation and transcriptional initiation, whereas TFIIA, TFIIE, and TFIIH are not required under certain conditions.   In addition, the PIC is stable in the absence of nucleotide triphosphates, and sequential addition of GTFs results in a series of partial PICs.  Here, we analyze the roles of all GTFs in yeast cells by measuring PIC formation and Pol II transcription upon depletion of individual GTFs.  All GTFs are essential for TBP binding and Pol II transcription in vivo, suggesting that partial PICs composed of GTF subsets do not exist at appreciable levels.   In contrast, TBP-associated factors (TAFs) contribute to Pol II transcriptional activity at most (and perhaps all) genes, but TAF-independent transcription occurs at a substantial level, particularly at promoters lacking canonical TATA elements.  Lastly, unlike the case in vitro, PICs are not observed in cells deprived of uracil, and presumably UTP, suggesting a mechanism that removes transcriptionally inactive PICs from promoters.

overall_design: Pol II occupancy is examined genome-wide by Chip-seq before and after the anchor-away of various General Transcription Factor subunits, as well as subsequent verification by qPCR and other follow-up experiments

first: Yi

last: Jin

first: Liguo

last: Dong

first: Koon

middle: H

last: Wong

first: Kevin

last: Struhl


title: Gene expression microarray analysis on the medial prefrontal cortex of wild-type mice (2W and 12W)

status: Public on Feb 25 2019

city: Toyoake

first: Hideo

last: Hagihara

address: 1-98 Dengakugakubo, Kutsukake-cho

department: Institute for Comprehensive Medical Science

institute: Fujita Health University

summary: The gene expression patterns in the medial prefrontal cortex of wild-type mice (2W and 12W) were examined using Affymetrix GeneChip arrays.

overall_design: Medial prefrontal cortex RNA isolated from C57BL/6J mice (2W, n = 6; 12W, n = 6).


title: Genomic copy number variation in head and neck squamous cell carcinoma cell lines

city: Ann Arbor

first: Chad

last: Brenner

state: Michigan

address: 1500 E Medical Center Drive / Cancer Center 6430

institute: University of Michigan

summary: Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer world wide, and survival rates range from 40-80% depending on subsite.  As novel treatment strategies are investigated, comprehensively characterized cell lines representative of the diversity seen in patients will be crucial to correlating genetic and phenotypic features with therapeutic response.  The University of Michigan has generated a large panel of HNSCC cell lines that are utilized in laboratories worldwide.  Here, we performed Oncoscan array analysis for 33 of these cell lines along with 2 HNSCC lines derived elsewhere to inform selection of model systems for future studies.

overall_design: Copy number analysis of Affymetrix OncoScan arrays was performed on 35 HNSCC cell lines.

first: J

middle: C


title: The Arabis alpina APETALA2 orthologue delays flowering by repressing floral meristem identity genes during vernalization

city: Köln

first: Maria

last: Albani

address: Carl-von-Linné-Weg 10

department: Botanical institute

institute: University of Cologne

summary: PEP2 regulates flowering in response to vernalization in a PEP1 -dependent and PEP1-independent pathway

overall_design: Arabis alpina Pajares wild-type, pep1-1 and pep2 mutants plants were grown under control condition, their shoot apices were dissected and analyzed for mRNA abundances using RNA-sequencing.

first: Ana

last: Lazaro

first: Yanhao

last: Zhou

first: Miriam

last: Giesguth

first: Kashif

last: Nawaz

first: Sara

last: Bergonzi

first: Ales

last: Pecinka

first: George

last: Coupland


title: Genome wide transcriptional response to altered levels of the Rpb7 subunit of RNA polymerase II identifies its role in DNA damage response in Schizosaccharomyces pombe

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

institute: Genotypic Technology

summary: RNA Pol II is a highly conserved and multisubunit protein complex composed of 12 different subunits. Rpb4 and Rpb7 are small subunits and uniquely present in RNA Pol II in eukaryotes. Rpb7 is essential and highly conserved protein among all eukaryotes. However, we have a limited understanding of the functions of Rpb7 subunit. Therefore, in the present study, we have used whole genome microarrays to compare the transcriptional response of S. pombe cells expressing low levels of rpb7+ with wild type cells.

overall_design: Organism : Schizosaccharomyces pombe, Agilent's S. pombe GXP Expression  8x15k Array (AMADID: 067936)

first: Deepak

last: Kumar

first: Nimisha

last: Sharma

first: Bipin

last: Chand


title: Sox11 induces cell aggregation and growth suppression in early progenitor B-cells

city: Huddinge

first: Martin

last: Lord

address: Alfred Nobels Alle 8

department: Institutionen för Laboratoriemedicin Avdelningen för patologi

country: Sweden

institute: KI

summary: The non-malignant, IL-3 dependent pro-B cell line Ba/F3 has previously been used for assessing transformation capability of oncogenes. We investigated functional and transcriptional changes in Ba/F3 cells upon Sox11 induction and find that the transcription factor Sox11 in this cellular background did not act as an oncogene.

overall_design: Cells were transduced with a retroviral TetON system carrying the murine Sox11 CDS (SOX11-ON with dox and SOX11-OFF without dox) and investigated for different factors. As additional control, non-transduced cells were cultured with dox (NT-ON) or without dox (NT-OFF)

first: Gustav

last: Arvidsson

first: Agata

middle: M

last: Wasik

first: Birger

last: Christensson

first: Anthony

last: Wright

first: Alf

last: Grandien

first: Birgitta

last: Sander


title: Transcriptomic analysis of reduced sensitivity to praziquantel in Schistosoma mansoni

city: Albuquerque

first: Charles

last: Cunningham

state: New Mexico

address: 1 University of New Mexico

department: Biology

institute: University of New Mexico

summary: Schistosomiasis is a chronic neglected tropical disease caused by digenetic parasitic flatworms of the genus Schistosoma. The disease is estimated to affect over 206 million people, the majority of whom live in Africa where Schistosoma mansoni and Schistosoma japonicum are the major causative agents. While a number of drugs have been used to treat schistosomiasis, praziquantel (PZQ) is the only one that is widely available, relatively cheap, and easy to use. The reliance on a single drug for the treatment of such a prevalent disease is a cause for concern due to the potential for resistance to render PZQ ineffective. In this study we examine the transcriptome of three generations of a laboratory strain of S. mansoni (PR1) whose susceptibility to PZQ has been diminished across 9 passages through exposure to increasing sub-lethal doses of the drug. Miracidial susceptibility was significantly reduced after exposure to 2 x 50 mg/Kg PZQ during the first passage. Susceptibility of worms in vivo was first assessed during passage 5 when mice infected with PZQ-selected schistosomes were dosed with a lethal dose of 3 x 300 mg/Kg PZQ resulting in only a 10% reduction in worm number compared to control treatment. The emergence of reduced sensitivity was marked by a shift in sex ratio from a predominantly male to female population, a reduction in the length of females and ultimately the loss of the PZQ-selected line after passage 9, perhaps due to a selection induced fitness cost. Analysis of differentially regulated transcripts did not suggest that any particular gene product or pathway was associated with drug resistance suggesting either a loss of function mutation to a single gene or an epistatic interaction of multiple gene products.

overall_design: Examination of  lab selected PZQ resistant Schistosoma mansoni parasites, in quadruplicate, through 3 passages using Illumina NextSeq 500.

first: Melissa

last: Sanchez


title: Gene expression microarray analysis on the medial prefrontal cortex of Camk2a+/- mice and wild-type mice

first: Hideo

last: Hagihara

summary: The gene expression patterns in the medial prefrontal cortex of Camk2a+/- mice and wild-type mice were examined using Affymetrix GeneChip arrays.

overall_design: Prefrontal cortex RNA isolated from Camk2a+/- mice (n = 6) or wild-type mice (n = 6)


title: Gene expression in STING-/- MEF cells expressing STING R284S variant

last: Griswold

summary: STING R284S variant is constitutively active and induces inflammatory genes even in absence of STING ligand cGAMP.

overall_design: Wild-type STING, N154S (SAVI mutant) and R284S were expressed in STING-/- MEF cells. RNA was extracted from the MEF cells and Affymetrix microarray was used to analyze gene expression in the MEF cells.

first: Hiroyasu

last: Konno


title: The genes differentially expressed in human colon cancer cells LoVo stably transfected with LV-control and LV-miR-500a respectively.

first: jide

last: Wang

summary: Microarrays were used to screen differentially expressed genes in LoVo stably transfected with LV-control and LV-miR-500a.

overall_design: In the experiments, we used the chip to detect the probe signal values of LoVo cells stably transfected with LV-control and LV-miR-500a, set 3 replicates per group, and then used Lv-control as a control to screen for genes that were up- or down-regulated simultaneously in LoVo cells stably transfected with LV-control and LV-miR-500a.

first: Jide


title: PTENα/β paradoxically promote carcinogenesis through WDR5-H3K4me3 axis [ChIP-seq]

city: shanghai

first: ge

last: mengkai

state: State...

address: shanghai

institute: Shanghai Jiao Tong University School of Medicine (SJTU-SM)

summary: we report that USP9X and FBXW11 selectively regulate the stability of PTENα/β but not PTEN proteins by deubiqitination and ubiquitination respectively. USP9X promotes and FBXW11 suppresses tumorigenesis mediated by PTENα/β. In contrast to the current paradigm for PTEN as a tumor suppressor, PTENα/β promote tumorigenesis of cancer cells in a phosphatase-independent manner. Mechanistically, PTENα/β localized in the nucleus regulate expressions of tumor-promoting genes such as NOTCH3 in the similar way as the H3K4 presenter WDR5. Further, PTENα/β but not PTEN directly interact with WDR5 to promote trimethylation of H3K4 and maintain a tumor-promoting signature.

overall_design: To confirm the interplay between PTENα/β and WDR5 at gene promoters using by ChIP seq in SMMC-7721

first: Shao-Ming

last: Shen

first: Cheng

last: Zhang

first: Meng-Kai

last: Ge

first: Shuang-Shu

last: Dong


title: Transcriptomic Profiling of Trophoblast Fusion Using BeWo and JEG-3 Cell Lines

city: Karachi

first: Muhammad

middle: Furqan

last: Bari

state: Sindh

address: Suparco Road, Ojha campus

department: Department of Pathology

country: Pakistan

institute: Dow University of Health Sciences

summary: Introduction: In human placenta, alteration in trophoblast differentiation has a major impact on placental maintenance and integrity. Moreover, abnormal syncytial fusion seems to be implicated in the development of many complications including pre-eclampsia and intra-uterine growth restriction (IUGR). However, little is known about the mechanisms that control cytotrophoblast fusion into syncytiotrophoblast. BeWo cell line is commonly used to study placental function since it can be induced to form syncytium and secretes hormones. This fusion is triggered by cAMP or forskolin treatments. In contrast, JEG-3 cell line fails to undergo substantial fusion. Therefore, we will use BeWo and JEG-3 cells to identify a set of genes responsible of trophoblast fusion.  Methods: BeWo and JEG-3 cells were treated with forskolin for 48 to induce fusion. RNA was extracted, hybridized to Affymetrix HuGene ST1.0 arrays and analyzed using system biology. Trophoblast differentiation was evaluated by real time PCR and immunocytochemistry analysis. Moreover, some of the identified genes were validated by real time PCR.     Results: Our results identified a list of 32 altered genes in fused BeWo cells compared to JEG-3 cells after forskolin treatment. Among these genes, 4 were validated by real-time PCR including salt inducible Kinase 1 (SIK1) gene which is specifically upregulated in BeWo cells upon fusion. Moreover, using system biology analysis, SIK1 showed to be at the center of many biological and functional processes which suggest that it might play a major role in trophoblast differentiation.   Conclusion: This study identified new target genes implicated in trophoblast fusion; a process implicated in the etiology of many pregnancy-related diseases such as preeclampsia, IUGR, and gestational diabetes.

overall_design: Effect of forkolin treatment on JEG-3 and BeWo cell lines

first: Firas

last: Kobeissy

first: Samer

last: El Hayek

last: Furqan Bari

first: Wassim

last: Abou-Kheir

first: Manu

last: Vatish

first: Georges

last: Daoud


title: Development and characterization of two canine melanoma cell lines with distinct clinical profiles: new models for comparative oncology

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

type: Genome variation profiling by genome tiling array

summary: In order to develop a new canine model of melnoma, we isolated and characterised three cell lines from oral canine malignant melanoma samples obtained from patients presenting distinct clinical behavior

overall_design: Total DNA was extracted from tumor tissues, the isolated cell lines and respective blood samples of each patient for the control. Our results highlight genomic melanoma alterations in accordance with the published litterature (Poorman et al, 2015; Gillard et al, 2014) and profiles reflecting the aggressivness and clinical evolution of each tumor.

first: Z

last: Segaoula

first: F

last: Lepretre

first: B

last: Hedan

first: E

last: Bouchaert

first: K

last: Minier

first: L

last: Marescaux

last: Serres

last: Quesnel

first: X

last: Thuru

first: D

last: Tierny


title: Gene expression microarray analysis on the medial prefrontal cortex of mice chronically treated with fluoxetine

first: Hideo

last: Hagihara

summary: The gene expression patterns in the medial prefrontal cortex of wild-type mice treated with fluoxetine (15 mg/kg/day for 3 weeks) or vehicle were examined using Affymetrix GeneChip arrays.

overall_design: Medial prefrontal cortex RNA isolated from wild-type mice (C57BL/6J) treated with fluoxetine (n = 8) or vehicle (n = 8).


title: Transcriptome characterization of Penicillium expansum induced by Meyerozyma guilliermondii

status: Public on Feb 28 2019

city: Zhenjiang

first: Qiya

last: Yang

address: Xuefu ROAD 301

institute: Jiangsu University

summary: Antagonistic yeasts inhibit the growth of fungal. In our previous research, Meyerozyma guilliermondii one of antagonistic yeasts exhibits antagonistic activity against Penicillium expansum. However, the mechanisms, especially the molecular mechanisms of inhibiting activity of M. guilliermondii are not clear. In this study, the transcriptome characterization of P. expansum induced by M. guilliermondii were investigated.

overall_design: Penicillium expansum induced with Meyerozyma guilliermondii and the control which was not induced with  Meyerozyma guilliermondii

first: Kaili

last: Wang


title: PTENα/β paradoxically promote carcinogenesis through WDR5-H3K4me3 axis [RNA-seq]

first: ge

last: mengkai

overall_design: RNA sequencing in parental and PTENα/βKO-1 SMMC-7721 cell lines with or without USP9X depletion by two independent experiments;   RNA sequencing in MiaPaCa2 cell lines with or without PTENα/β

first: Shao-Ming

last: Shen

first: Cheng

last: Zhang

first: Meng-Kai

last: Ge

first: Shuang-Shu

last: Dong


title: De novo mutation in ELOVL1 causes ichthyosis, acanthosis nigricans, and hypomyelination with lower extremity spastic paraplegia, high frequency deafness, and tunnel vision.

city: Berlin

first: Markus

last: Schuelke

state: Berlin

address: Augustenburger Platz 1

department: Neuropediatrics

institute: Charite

summary: We have compared the transcriptome of cultured human fibroblasts from 2 patientes with a mutation in the ELOVL1 gene with the transcriptome of four healthy age-matched controls.

overall_design: RNA-Seq transcriptome analysis of 2 patients and of 4 controls with a sequencing depth of >60 Mio reads.


title: Expression data from sorted mouse postnatal day 2 lung alveolar type 2 cells

city: Cambridge

first: Charles

last: Bradshaw

address: Tennis Court Road

institute: University of Cambridge

summary: We purified the differentiating alveolar type 2 cells from postnatal day 2 mouse lungs and used Affymetrix microarrays to obtain their gene expression profiles.

overall_design: Ciliated cells were isolated by flow cytometry as GFP+ cells from SpC-GFP mouse lungs at P2

first: Emma

last: Rawlins


title: Altered cell signaling in the absence of Dynamin function: a transcriptomic approach from yeast to humans (yeast)

status: Public on Feb 24 2019

city: Sevilla

first: Eloisa

last: Andujar

state: Sevilla

address: Avda Americo vespucio s/n

department: GENOMICS UNIT

country: Spain

institute: CABIMER-CSIC

summary:
Dynamins are large multidomain GTPases involved in membrane scission. We have investigated the transcriptional consequences of deleting Vps1, a DNM2 homologue, in the yeast Saccharomyces cerevisiae. Interestingly, the vps1∆ mutation causes strong transcriptional defects also in yeast.
Data suggest that DNM2 and Vps1 play an essential regulatory role connecting several membrane-related processes including endocytosis, lipid homeostasis and different signal transduction pathways.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: Transcriptomic data from wild type and vps1Δ strains under normal growth conditions were compared. Three biological independient replicates were use for each strain.

first: Macarena

last: Morillo-Huesca

first: Maria

middle: S

last: Dominguez-Sanchez

first: Tatiana

last: Alfonso-Perez

first: Monica

last: Perez-Alegre

first: Valentina

last: Bachetti

first: Mario

last: Garcia-Dominguez

first: Jose

last: Reyes


title: MIR205HG- and miR-205- knockout mice comparisons of gene expression in the epithelial tissues of the skin and from the pituitary

status: Public on Feb 23 2019

city: Dallas

first: Igor

last: Dozmorov

state: TX

address: 5323 Harry Hines Blvd

department: Immunology

institute: UT Southwestern Medical Center

summary:
RNA was isolated from mouse skin and pituitary. This was used for gene comparisons with an affymatrix Clariom S array
We compared the differences in transcripts expressed in the skin and the pituitary in the presence/absence of MIR205HG- and miR-205, which revealed significant differences in the pituitary and overlap in the skin

first: Nicolai

last: van Oers


title: Expression data from C. elegans exposed to  pristine and aged ZnO manufactured  nanoparticles

status: Public on Feb 22 2019

city: Lexington

first: Olga

last: Tsyusko

state: KY

address: 1100 S. Limestone St

institute: University of Kentucky

summary:
Caenorhabditis elegans were exposed at EC30 for 48 hr at L1 stage to ZnSO4,  pristine ZnO-MNPs, phosphate aged pZnO-MNPs and sulfidized sZnO-MNPs
Whole genome whole trascript microarrays were used to examine and compare global gene expression profiles among treatments

overall_design: There were 3 replicates (age synchronized plates of the exposed worms) per treatment with 5 treatments total including controls

first: Daniel

last: Starnes


title: Low-input chromatin profiling in Arabidopsis endosperm using CUT&RUN

first: Xiao-yu

last: Zheng

address: 455 Main Street

institute: Whitehead Institute for Biomedical Research

summary: Endosperm is an essential seed tissue with a unique epigenetic landscape. During endosperm development, differential epigenetic regulation of the maternal and paternal genomes plays important roles in regulating gene expression, especially at imprinted genes. Profiling the endosperm epigenetic landscape on a genome-wide scale is challenging due to its small size, mode of development, and close association with maternal tissue. Here, we applied a low input chromatin profiling method, CUT&RUN (cleavage under targets and release using nuclease), to profile parental-specific chromatin modifications using low numbers of Arabidopsis endosperm nuclei. We demonstrate that CUT&RUN generates genome-wide H3K27me3 landscapes with high sensitivity, specificity and reproducibility using around 20,000 endosperm nuclei purified by flow cytometry and fluorescence-activated cell sorting. H3K27me3 peaks identified by CUT&RUN and previous ChIP (chromatin immunoprecipitation) approaches were largely overlapping, with some distinctions in heterochromatin. The versatility and simplicity of CUT&RUN makes it a viable alternative to ChIP, which requires greater amounts of starting material, and will enable the study of tissue or even cell-type specific epigenomes in Arabidopsis and other plant species.

overall_design: Col plants were emasculated and pollinated by Ler pollens two days later. Seeds were removed from siliques and nuclei from these seeds were extracted using Partec CyStain UV Precise P and immediately FACS sorted based on DAPI. For test experiments using seed coat and embryo nuclei, seeds were removed from siliques sever days after pollination. 2N, 4N and 8N nuclei were collected for CUT&RUN with anti H3K27me3 antibodies or no antibody. For endosperm CUT&RUN, seeds were removed from siliques four days after pollination (embryo at globular stage). 6N nuclei were collected for CUT&RUN either directly without formaldehyde fixation (Unfixed) or after formaldehyde fixation (Fixed). Anti H3 or H3K27me3 antibodies were used in CUT&RUN to profile H3, H3K27me3 landscapes. Normal rabbit IgG were used to generate negative control data. For leaf CUT&RUN, leaves were taken from 3-week-old Col plants. Leaf nuclei was extracted using Partec CyStain UV Precise P for FACS sorting and 2N, 4N and 8N nuclei were collected for CUT&RUN. Endosperm CUT&RUN sequencing samples are designated Endo_{fixation}_{antibody}_N, where fixation = Unfixed or Fixed; antibody = H3, H3K27me3 or IgG; N = the replicate number (either 1 or 2). Seed coat and embryo CUT&RUN sequencing samples are designated 2N_{antibody}_{nuclei number}_{digestion time} , where antibody= H3K27me3 or noab (no antibody). Leaf CUT&RUN sequencing samples are designated Leaf_{antibody}, where antibody= H3, H3K27me3 or IgG.

first: Mary

last: Gehring


title: Gene expression profiling of the Arabidopsis Mediator MED5 mutants ref4-1 and ref4-3, CDK8 mutant cdk8-1 and ref4-3 cdk8-1

city: West Lafayette

first: Clint

last: Chapple

state: IN

address: 175 S. University St.

department: Department of Biochemistry

institute: Purdue University

summary:
Purpose:  To identify changes in gene expression in ref4-3 mutant that contribute to the mutant’s altered growth and metabolite accumulation by comparing differential gene expression in ref4-3 and ref4-3 cdk8-1.
Methods: Gene expression profiles were generated from 20-day-old, pooled Arabidopsis rosettes in biological triplicate, by paried-end sequencing of 100 bp fragments using Illumina HiSeq 2500. The sequence reads that passed quality filters were aligned to the TAIR10 reference genome using TopHat. Gene counts were determined using HTseq-count. Differential expression analysis was performed using edgeR.
Results: We identified 7,355 genes that were differentially expressed in ref4-3 compared to wild type, part of which were significantly rescued by loss of CDK8 (FDR <0.05).

overall_design: Gene expression profiles of wild type and Mediator single or double mutants were generated in biological triplicate from 20-day-old Arabidopsis rosettes by deep sequencing using Illumina HiSeq 2500.

first: Xiangying

last: Mao


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and dek44 mutant Transcriptomes

city: Shanghai

first: weiwei

last: Qi

address: No 99 Shangda Road

institute: Shanghai  University

summary: Analysis of  gene expression level. The hypothesis tested in the present study was that dek44 mutant influence the expression of mitochondrial ETC associated genes. Results provide important information of the gene expression level regulation of mitochondrial envelop, proton transport,translation and genes associated with other biological processes.

overall_design: Endosperm mRNA profiles of 15DAP wild type (WT) and dek44 mutant were generated by deep sequencing, in triplicate, using Illumina Hiseq 2500 (Zea mays).

first: Weiwei

first: Lei

last: Lu


title: Gene expression of mesothelioma cell line ACC-Meso-4 treated with shRNA targeting chromobox (CBX) 6, 7, and 8.

city: Kanazawa

first: Takumi

last: Nishiuchi

address: 13-1 Takaramachi

institute: Kanazawa University

summary: Chromobox (CBX) family proteins are components in polycomb repressive complex 1 (PRC1), responsible for targeting PRC1 to the chromatin. We studied genes regulated by CBX6, 7, or 8 in human ACC-Meso-4 mesothelioma cell line by microarray analysis of ACC-Meso-4 cells stably expressing short hairpin RNA (shRNA) targeting CBX-6, 7, 8, or control nontarget shRNA.

overall_design: Total RNA was prepared respectively from ACC-Meso-4 cells stably expressing shRNA targeting CBX6, 7, 8, or nontarget. RNA samples (n=2 for each groups) were subjected to microarray analysis, using the Agilent Whole Human Genome 8X60k Oligo Microarray (Agilent Technologies).

first: Katsuya

last: Sakai

first: Kunio

last: Matsumoto


title: Beadarray expression analysis to identify how LILRB2 blockade may affect transcriptional networks in M(LPS) and M(IL4)

city: Houston

first: HUIMING

last: CHEN

state: Texas

address: 1613 Wheeler St

institute: Houston Methodist Research institute

summary: We performed Illumina microarrays to identify how LILRB2 blockade may affect transcriptional networks in M(LPS) and M(IL4). To compare M(LPS) and M(IL4) populations helped define markers and pathway networks associated with M1 vs. M2-like functional phenotypes

overall_design: The expression levels of transcripts in human purified CD33 myeloid cells treated with antiLILRB2 antagonistic antibody and control Ig in the presence of IL4 or LPS. Three independent replicates from three healthy donors were analyzed for each condition.

first: William

last: Van Der Touw

first: Shu-Hsia

last: Chen


title: Altered cell signaling in the absence of Dynamin function: a transcriptomic approach from yeast to humans (human)

first: Eloisa

last: Andujar

summary:
Dynamins are large multidomain GTPases involved in membrane scission. We have investigated the transcriptional consequences of deleting DNM2 by siRNA in HeLa cells. Interestingly, DNM2 depletion causes strong transcriptional defects.
Data suggest that DNM2 playes an essential regulatory role connecting several membrane-related processes including endocytosis, lipid homeostasis and different signal transduction pathways.

overall_design: HeLa cells were transfected with control siRNA (siControl) or siRNA against DNM2 (siDNM2) and samples were taken after 24 h or 72 h. Three independent samples were taken from each condition.

first: Maria

last: Dominguez-Sanchez

first: Tatiana

last: Alfonso-Perez

first: Macarena

last: Morillo-Huesca

first: Monica

last: Perez-Alegre

first: E

first: V

last: Bachetti

first: Mario

last: Garcia-Dominguez

first: C

last: Reyes


title: Gene expression profiles of TN breast tumors

city: Toronto

first: Benjamin

last: Haibe-Kains

address: 610 University Avenue

department: Princess Margaret Research

institute: Princess Margaret Cancer Centre

summary: Engaging the immune system promises to be key for optimal cancer therapy, especially in hard-to-treat disease such as triple-negative breast cancer (TNBC). However, the immune microenvironment remains poorly understood. Using gene expression based on laser capture microdissection, we identify three distinct tumor microenvironments associated with CD8+ T cell localization patterns and outcome in TNBC. An immunoreactive microenvironment is defined by granzyme B-positive CD8+ T cell infiltration, a type I interferon signature,  tumor expression of PD-L1 and good outcome. In contrast, tumors with an immune-cold microenvironment display restriction of CD8+ T cells to tumor margins, elevated tumor expression of the immunosuppressive marker B7-H4, a signature of desmoplastic stroma and poor outcome. A third distinct immunomodulatory microenvironment associated with poor outcome is enriched for IL-17-producing cells and neutrophils, as well as stroma-restricted localisation of CD8+ T cells. These distinct immune microenvironments have implications for TNBC patient stratification for current and future therapies.

overall_design: 37 patient samples; each subjected to gene expression profiling using Affymetrix Human Gene 1.0 ST Array

first: Morag

last: Park


title: Expression data from embryonic day 16.5 or postnatal day 3 mouse liver

status: Public on Feb 21 2019

city: Onna

first: Toru

last: Suzuki

state: Okinawa

address: 1919-1 Tancha

institute: Okinawa Instutue of Science and Technology Graduate University

summary:
mRNA degradation critically contributes to liver development and function. The CCR4-NOT complex serves as a major deadenylase that initiates mRNA degradation.
We used microarrays to identify deregulated genes in the livers lacking Cnot3, a core subunit of the CCR4-NOT complex.

overall_design: Liver-specific Cnot3 knockout mice were generated by expressing Cre recombinase under the control of Albumin promoter. Livers from control and CNOT3 knockout mice were used for RNA extraction and hybridization on Affymetrix microarrays.

first: Chisato

last: Kikuguchi


title: Gene expression profiles of microdissected tumor  epithelium and stroma from TN breast tumors

overall_design: 38 patient samples, tissue compartments isolated by laser capture microdissection to yield 38 samples of tumor epithelium, 38 samples of tumor stroma; each subjected to gene expression profiling in a common reference design using Agilent whole human genome oligonucleotide arrays.


title: Expression data from 4-week-old mouse liver

summary:
mRNA degradation critically contributes to liver development and function. The CCR4-NOT complex serves as a major deadenylase that initiates mRNA degradation.
We used microarrays to identify deregulated genes in the livers lacking CNOT3, a core subunit of the CCR4-NOT complex.

overall_design: Liver-specific CNOT3 knockout mice were generated by expressing Cre recombinase under the control of Albumin promoter. Livers from control and CNOT3 knockout mice were used for RNA extraction and hybridization on Affymetrix microarrays.


title: Expression data from 3D cell-printed human bone marrow derived mesenchymal stem cells (hBMMSCs) with liver, heart, skin and cornea decellularized extracellular matrix (dECM) bioinks

city: Pohang

first: Dong-woo

last: Cho

state: Gyeongbuk

address: 77 Cheongam-ro, Nam-gu

department: Department of Mechanical Engineering

country: South Korea

institute: POSTECH

summary:
Whole transcriptome profiling of hBMMSCs printed with various dECM bioinks were conducted to reveal the effect of compositional variations in a tissue-specific manner
Differential expression patterns of genes were observed in a tissue-specific manner, and this research provides strong evidence of the tissue-specific functionalities of dECM bioinks.

overall_design: hBMMSCs were 3D-cell printed with liver, heart, skin, and cornea dECM bioink, he cell-laden constructs were printed using an in-house-developed 3D cell printing system. Cell-printed constructs were incubated at 37°C for 30 minutes to induce thermal crosslinking. The cell-printed constructs were cultured for seven days in the same culture media condition. Each group was duplicated, and each trial was in average with 6 samples

first: Wonil

last: Han

first: Narendra

middle: K

last: Singh


title: Dose-responsive transcriptomic profiles in mahi-mahi (Coryphaena hippurus) larvae exposed to Deepwater Horizon oil (mRNA profiles)

status: Public on Feb 20 2019

city: Riverside

first: Genbo

last: Xu

address: 900 University Ave

institute: University of California, Riverside

summary:
Purpose:To help identify molecular mechanisms and pathways potentially involved in the developmental toxicity for fish exposed to different concentrations of Deepwater Horizon (DWH) oil, transcriptomic profiles in mahi-mahi (Coryphaena hippurus) embryos exposed to different DWH oils (source and artificially weathered oil) were evaluated  using High Throughput Sequencing (HTS).
Methods:Total mRNA profiles of 48 hpf mahi-mah larvae after slick (0.5%, 1%, and 2%)  and source/mass oil (0.125%, 0.25% and 5%) exposure were generated by deep sequencing, in triplicate, using Illumina NextSEQ v2.
Results:To determine the potential biological impact of oil exposure at system level, a gene ontology (GO) term analysis on biological processes (BPs) was conducted by analyzing the DEGs using ToppGene. The profile of BPs was dose- and oil type- dependent.  After exposure to 0.125% slick oil, the top enriched biological processes were RNA processing and RNA metabolism terms. Metabolic and catabolic process and terms associated with embryo development were some of the most enriched BPs at 0.25% slick oil. The top enriched BPs at 0.5% slick oil were organic acid metabolic process and cardiovascular system development.  For source oil, cell cycle process, metabolic process, and RNA processing were the most enriched by 0.125% source oil exposure, which were also highly enriched by 0.25% source oil exposure, while more ‘response’ BPs were enriched by 0.25% source oil exposure, such as regulation of response to stress, response to endogenous stimulus, response to hormone, cellular response to light stimulus, etc.  The most significantly enrich BP by 0.5% source oil was cardiovascular system development followed by organic acid metabolic process and cell junction assembly.

overall_design: Total mRNA profiles of 48hpf mahi-mah larvae after slick and source oil exposure were generated by deep sequencing, in triplicate, using Illumina NextSEQ v2.

first: Elvis

middle: G

first: Jason

middle: T

last: Magnuson

first: Edward

last: Mager

first: Martin

last: Grosell

first: Graciel

last: Diamante

first: Aaron

middle: P

last: Roberts

first: Daniel

last: Schlenk


title: Panomics analysis of lipid metabolism in X-ALD

city: Seoul

first: Jiho

last: Jang

address: 50 Yonsei-ro Seodaemoon-gu

department: Department of Physiology

institute: Yonsei University College of Medicine

summary:
The Transcriptomic analysis of RNA samples from adrenomyeloneuropathy (AMN) and childhood cerebral adrenoleukodystrophy (CCALD), and healthy control
transcriptomics data was conducted to elucidate distinctive metabolic biosignatures among AMN and CCALD, and healthy control

overall_design: We analyzed 24 samples (8 sets of HDF, AMN, CCALD, respectively) using the Affymetrix GeneChip® HT HG-U133+ PM Array. Array data was processed by Affymetrix. Chp files were analyzed using the probe sets for the HG-U133A array.


title: Liver development requires Cnot complex-mediated decay of mRNAs encoding cell cycle, cell division, and immature liver genes

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

overall_design: Refer to individual Series


title: Transcriptional regulation of Hepatic Stellate Cell plasticity in NASH

city: Odense M

first: Kim

last: Ravnskjaer

state: CA

address: Campusvej 55

department: Department of Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: We here perform transcriptional profiling of hepatic stellate cells (HSCs) isolated from Western diet/high fructose-fed C57BL6/J mice, carbon tretrachloride (CCl4)-treated C57BL6/J mice, and of murine HSCs differentiated in vitro.

overall_design: Gene expression profiles from hepatic stellate cells isolated from C57BL6 mice fed a Western Diet supplemented with high fructose for 12, 16 or 24 weeks or normal chow. Gene expression profiles from hepatic stellate cells isolated from C57BL6 mice treated CCl4 for 1, 4 or 8 weeks or treated with vehicle. Gene expression profiles from hepatic stellate cells isolated from C57BL6 mice and seeded on normal plastic cell culture dishes for 1, 4, 8, or 12 days.

first: Ann-Britt

last: Marcher


title: Dose-responsive microRNA profiles in mahi-mahi (Coryphaena hippurus) larvae exposed to Deepwater Horizon oil

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose: To help identify molecular regulatory mechanisms of developmental toxicity for fish exposed to Deepwater Horizon (DWH) oil, microRNA profiles in mahi-mahi (Coryphaena hippurus) larvae exposed to different DWH oils (source/mass and artificially weathered oil) were evaluated  using High Throughput Sequencing (HTS).
Methods: Total microRNA profiles of 48 hpf mahi-mah larvae after slick (0.5%, 1%, and 2%)  and source/mass oil (0.125%, 0.25% and 5%) exposure were generated by deep sequencing, in triplicate, using Illumina NextSEQ v2.
Results: Among over 100 significant DE miRNAs, DE miRNAs that were inversely correlated with target mRNAs after slick and source oil exposure were identfied. miR-34b, miR-181b, miR-23b, and miR-203a responsive to both slick and source oil exposure were further filtered to predict downstream biological functions. The target genes of these four miRNAs were involved AhR signaling, Cardiac β-adrenergic signaling, nNOS signaling in neurons, xenobiotic metabolism signaling, p53 signaling, cell cycle regulation, etc., as well as potential diseases including cardiovascular disease, neurological disease, developmental disorder, ophthalmic disease, metabolism disease, etc.

overall_design: Total microRNA profiles of 48hpf mahi-mahi larvae after slick and source oil exposure were generated by deep sequencing, in triplicate, using Illumina NextSEQ v2.


title: Differential Gene Expression between involved and uninvolved sites of Crohn’s disease: Insights into a Distinctive Pathogenesis Profile

city: Guangzhou

first: Xinmei

last: Zhao

address: No 1838 Guangzhou North Avenue

institute: Nanfang Hospital, Southern Medical University

summary:
Our objective was to elucidate patterns of gene expression underlying the progression of CD disease.
Surgery biopsies (n=60) were assayed using the Illumina cDNA-mediated Annealing, Selection, Extension, and Ligation (DASL) microarray process specifically designed for use with Formalin-Fixed, Paraffin-Embedded (FFPE) clinical samples. Tissue was sampled in consecutive active involved and uninvolved sites at the same time in individual CD patients, and these samples (CD involved and CD uninvolved) were compared with each other as well as to non-inflammatory bowel disease (non-IBD) healthy controls.

overall_design: Gene expression of CD involved and uninvolved is compared at a global level using total RNA from the same CD pateints using the Illumina microarray platform.


title: Expression data from fetal hepatocytes from control or Cnot3KO E16.5 embryos treated with Actinomycin D for 0, 6 or 12h

first: Toru

summary:
mRNA degradation critically contributes to liver development and function. The CCR4-NOT complex serves as a major deadenylase that initiates mRNA degradation.
We used microarrays to identify abnormally stabilized mRNAs in the fetal hepatocytes lacking Cnot3, a core subunit of the CCR4-NOT complex.

overall_design: Liver-specific Cnot3 knockout (Cnot3LKO) mice were generated by expressing Cre recombinase under the control of Albumin promoter. Fetal hepatocytes were prepared from embryos after crossing control or Cnot3LKO mice. Total RNAs were prepared before or after Actinomycin D treatment and used for hybridization on Affymetrix microarrays.


title: DNA methylation and gene expression after decreased CTCF expression in human prostate epithelial cells

city: Madison

first: Nathan

last: Damaschke

state: WI

address: 1111 Highland Ave Room 7048

department: Urology

institute: University of Wisconsin

type: Methylation profiling by genome tiling array


title: Expression data from short hairpin RNA mediated CTCF knockdown in human prostate epithelial cells

summary: Transcriptional profiling of immortalized human prostate epithelial cells after CTCF knockdown by short hairpin RNA.  Knockdown by shRNA targeting CTCF was conducted for 5 days by addition of doxycycline to induce shRNA expression.  RNA was purified from triplicate biological replicates of induced and uninduced shRNA samples.  Gene expression was quantified by hybridization to Affymetrix Human Transciptome 2.0 arrays.

overall_design: Triplicate samples of induced and uninduced shRNA targeting CTCF were used to quantify the effects of CTCF knockdown on genome wide gene expression.  Cells were treated with either doxycycline to induce shRNA, or uninduced vehicle only control using DMSO.  Raw .CEL files were analyzed using the Affymetrix Transcriptome Analysis Console (v3.0).  Triplicate samples were compared using the t-test, followed by False Discovery Rate (FDR) adjustments.

first: N

first: D

middle: F

last: Jarrard


title: Expression data from 1-week-old mouse liver

last: Suzuki

first: Chisato

last: Kikuguchi


title: Enhanced cardiac reprogramming by Inhibition of cyclooxygenase-2/prostaglandin E2/prostaglandin E receptor 4 signaling

city: Tokyo

first: Naoto

last: Muraoka

address: 35 Shinanomachi, Shinjuku-ku

department: Department of Cardiology

institute: Keio University School of Medicine

summary: Direct cardiac reprogramming from fibroblasts can be a promising approach for disease modeling, drug screening, and cardiac regeneration in pediatric and adult patients. However, postnatal and adult fibroblasts are less efficient for reprogramming compared with embryonic fibroblasts, and barriers to cardiac reprogramming associated with aging remain undetermined. In this study, we screened 8,400 chemical compounds, and found that diclofenac sodium (diclofenac), a non-steroidal anti-inflammatory drug, greatly enhanced cardiac reprogramming in combination with Gata4, Mef2c, and Tbx5 (GMT) or GMT plus Hand2. Intriguingly, diclofenac promoted cardiac reprogramming in mouse postnatal and adult tail-tip fibroblasts (TTFs), but not in mouse embryonic fibroblasts (MEFs). Mechanistically, diclofenac enhanced cardiac reprogramming by inhibiting cyclooxygenase-2, prostaglandin E2/prostaglandin E receptor 4, cyclic AMP/protein kinase A, and interleukin 1b pathway, silencing inflammatory and fibroblast programs, which were activated in postnatal and adult TTFs. Thus, anti-inflammation can be a new target for cardiac reprogramming associated with aging.

overall_design: We analyzed gene expression levels in GHMT-, GHMT/diclofenac-, GHMT/EP4 antagonist-, GHMT/diclofenac/PGE2-, GHMT/TGFb inhibitor- or GHMT/Wnt inhibitor-transduced TTFs by microarray (Clariom S Array, Mouse, Affymetrix) according to the manufacturer’s instructions. Prior to analysis, all data were normalized by using a Single Space Transformation and Robust Multichip Analysis (SST-RMA) algorithm with Affymetrix Expression Console software version1.4.

first: Masaki

last: Ieda


title: Decreased CTCF Expression Directs DNA Hypermethylation Events in Cancer

summary: Methylation profiling of immortalized human prostate epithelial cells after CTCF knockdown by short hairpin RNA.  Methylated DNA was immunoprecipitated with anti-methylcytosine antibodies from genomic DNA and detected by Affymetrix CytoScanHD chips.  Methylated DNA was purified by 5-mC antibodies and Affymetrix CytoScanHD arrays were performed according to the manufacturer's protocols.

overall_design: Copy number analysis of Affymetrix CytoScanHD arrays were performed and immunoprecipitated methylated DNA and matched input samples.  Input samples were used to normalize copy number variation specific effects.  Raw intensity data was extracted from .CEL files using Affymetrix Power Tools and normalized using RMA style background adjustment.  Log2 transformed values for input samples were subtracted from immunoprecipitated samples.  Each probe represents the probe detected by the Affymetrix CytoScan HD Array.

first: J

last: Luo

first: Y

last: Yu


title: Genomic Whole-Organ Map of Mucosal Field Effects Initiating Human Bladder Carcinogenesis

status: Public on Feb 19 2019

first: Hui

last: Yao

address: 1515 Holcombe Blvd.

department: Bioinformatics and Computational Biology

institute: MD Anderson Cancer Center

type: Methylation profiling by high throughput sequencing

summary: We have developed a whole organ mapping approach which combines microscopic assessment of the entire mucosal membrane of the organ affected by cancer with comprehensive genomic profiling.  It was used to study the chronology of the molecular changes in the human bladder as they evolved from mucosal field effect through dysplasia and carcinoma in situ to multifocal carcinoma.  The widespread methylation changes involving almost the entire mucosa were identified as a major mechanism driving the development of the initial field effect.  They also involved a small number of genomic amplifications and losses confirming the clonal nature of the initiating mucosal change. The mutations of the genes which included the activating mutation of Kras and an inactivating mutation of chromatin remodeling gene ACIN1 occured with the advent of carcinoma in situ and did not change with progression to frank carcinoma.  The development of carcinoma was associated with copy number gain as a dominant change.  A pattern of mutations and copy number changes in carcinoma in situ and several foci of carcinoma were almost identical confirming their clonal origin.  The integrated analysis disclosed a complex and accummulating pattern of alterations of multiple oncogenic pathways already evident in mucosal field change.  Strikingly the alterations of Kras effector pathways associated with invasion and migration were already present in the tissue field prior to the emergence of mutant Kras.  The whole organ mapping approach presented in this study provides novel clues for the understanding of occult mucosal changes that underlie bladder cancer development and have important implications for early detection, prevention and treatment.

overall_design: Mucosal samples from surgically removed bladder that contained multi-focal papillary bladder cancer were subjucted to whole exome sequencing, CNV  and methylation analysis

first: Tadeusz

last: Majewski

first: Jolanta

last: Bondaruk

first: Woonbok

last: Chung

first: Sangkyou

last: Lee

first: June

first: Shizhen

last: Zhang

first: David

last: Cogdell

first: Guoliang

last: Yang

first: Woonyoung

last: Choi

first: Colin

last: Dinney

first: H

middle: B

last: Grossman

first: Christopher

last: Logothetis

first: Steven

middle: E

last: Scherer

first: Charles

last: Guo

first: Li

first: Peng

last: Wei

first: John

middle: N

last: Weinstein

first: Jean-Pierre

last: Issa

first: Keith

last: Baggerly

last: McConkey

first: Bogdan

last: Czerniak


title: Mycobacterium tuberculosis transcriptional response to small molecule

city: Newark

first: Xin

last: Wang

address: 185 South Orange Avenue

institute: Rutgers University - New Jersey Medical School

summary: We applied RNAseq (Nextseq) technology to study mechanism of action of nitro-containing heterocycle antitubercular JSF-2019, with des-nitro JSF-2026 as control. Briefly, mid-log phase (OD = 0.3) M. tuberculosis culture was treated by 10x MIC of each compound in biological quadruplicates followed by mRNA extraction and RNAseq analysis. We find that JSF-2019 and pretomanid as intracellular NO• donors exhibited distinct transcriptional patterns comparing to extracellular iNOS inducer such as DETA/NO, therefore it suggests distinguished mechanisms of action between intracellular vs. extracellular NO• donors. We also observed that JSF-2019 upregulated a subset of FAS-II genes similar to isoniazid, indicating JSF-2019 inhibits intracellular mycolic acid biosynthesis.

overall_design: Examine M. tuberculosis gene expression at 10x MIC compound treatment for 4 hours.

first: Wang

last: Xin

first: Hussain

last: Seema


title: CRISPR/dCas-based modulation of bacterial IS-transposition

first: Balazs

last: Balint

state: Csongrad

address: Vallalkozok street

country: Hungary

institute: Seqomics Ltd

summary: In this work, a plasmid-based system is applied to inhibit the transposition of bacterial insertion sequences (IS). Using multiple guide RNAs, inactivated Cas9 was directed to simultaneously bind to the left end of IS1, IS5, IS3 and IS150 in Escherichia coli, in vivo. As a result, the transcription of IS1, and IS5 was successfully silenced, in certain cases by two orders of magnitude. The transposition rate of all four targeted elements nevertheless dropped to negligible levels, as verified at the cycA and bgl chromosomal loci. A GFP-expressing plasmid, known to be predominantly inactivated by insertion mutations also displayed a significant increase in stability. The transposition-silencing effect was easily transferable between various E. coli strains by plasmid transformation. Our portable system, or other plasmids constructed likewise can serve as useful tools to eliminate insertion mutagenesis or selectively study distinct transposable elements in numerous prokaryotic species.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: The transcriptome of three samples were analyzed originating from the IS-knockdown strain. Three controls were also analyzed from cells carrying a mock-silencing plasmid.

first: Ákos

last: Nyerges

first: Judit

last: Cseklye

first: Balázs

last: Bálint

first: István

last: Nagy

first: Csaba

last: Pál

first: Tamás

last: Fehér


title: The Hippo Pathway Prevents YAP/TAZ–Driven Hypertranscription and Controls Neural Progenitor Number [microarray]

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

summary: The Hippo pathway controls the activity of YAP/TAZ transcriptional coactivators through a kinase cascade. Despite the critical role of this pathway in tissue growth and tumorigenesis, it is not fully understood how YAP/TAZ–mediated transcription drives proliferation. By analyzing the effects of inactivating LATS1/2 kinases, the direct upstream inhibitors of YAP/TAZ, on mouse brain development and applying cell-number–normalized transcriptome analysis, we discovered that YAP/TAZ activation causes a global increase in transcription activity, known as hypertranscription, and upregulates many genes associated with increased biosynthetic capacity and proliferation. In contrast, conventional read-depth–normalized RNA-sequencing analysis failed to detect the scope of the transcriptome shift and missed most relevant gene ontologies. Hypertranscription in neural progenitors inhibits differentiation and triggers DNA replication stress, DNA damage, and p53 activation, resulting in massive apoptosis. Our findings reveal the remarkable impact of YAP/TAZ activation on global transcription activity and have important implications for understanding YAP/TAZ function

overall_design: We used microarrays to compare the gene expression profiles of cortices from control and Lats1F/F;Lats2F/F;Nestin-Cre double knock-out E12.5 mouse embryos.

first: Alfonso

last: Lavado

first: Jun

middle: Y

last: Park

first: Geoffrey

last: Neale

first: Xinwei

last: Cao


title: Burkitt-like lymphoma with 11q aberration: A germinal center derived lymphoma without ID3-TCF3-CCND3 pathway deregulation [ONCOSCAN]

city: Barcelona

first: Joan

middle: Enric

last: Ramiz-Zaldivar

address: Rosselló, 153

department: Molecular Pathology Laboratory

institute: IDIBAPS

summary: Burkitt-like lymphoma with 11q aberration (BLL-11q) is a new provisional category in the 2016 WHO classification. The limited number of reported cases does not allow to define whether this is a specific entity or it is a particular variant of other recognized categories such as Burkitt or diffuse large B-cell lymphoma.  The genetic alterations involved in the pathogenesis of BLL-11Q are not known.

overall_design:
The aim of this study was to perform a complete genetic characterization of Burkitt like lymphoma with 11q aberration. Eleven cases (8 males and 3 females; mean age: 15 years, range 8-37) with consensus diagnosis were analyzed by fluorescence in situ hybridization, copy number (CN) array and targeted sequencing analyses of genes associated with B-cell lymphoma pathology.
BLL11q_ONCOSCAN

first: Blanca

last: Gonzalez-Farre

last: Ramis-Zaldivar

first: Itziar

last: Salaverria


title: Burkitt-like lymphoma with 11q aberration: A germinal center derived lymphoma without ID3-TCF3-CCND3 pathway deregulation [SNP6]

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

overall_design:
The aim of this study was to perform a complete genetic characterization of Burkitt like lymphoma with 11q aberration. Eleven cases (8 males and 3 females; mean age: 15 years, range 8-37) with consensus diagnosis were analyzed by fluorescence in situ hybridization, copy number (CN) array and targeted sequencing analyses of genes associated with B-cell lymphoma pathology.
BLL11q_SNP


title: Defining the transcriptional signature of healing and non-healing lesions during murine cutaneous leishmaniasis

city: Philadelphia

first: daniel

last: beiting

state: PA

address: 380 S. University Ave

department: Pathobiology

institute: University of Pennsylvania

summary: Leishmaniasis is a group of diseases caused by parasites of the genus Leishmania that affects millions of people worldwide. The disease outcome is determined by both the parasite species and the host's immune response.  Leishmania major infection causes a localized cutaneous lesion in patients and has been widely used to study the development of T cell responses in mice.  L. major infected C57BL/6 mice are resistant to infection due to the development of Th1 responses, whereas BALB/c mice develop a Th2 response resulting in disease susceptibility and failure to control parasite replication.  However, these disparate host phenotypes are not observed with all Leishmania species.  For example, during L. braziliensis infection both BALB/c and C57BL/6 mice are resistant.  In order to better understand the host genetic basis underlying disease susceptibility in vivo, we performed a whole genome transcriptional analysis from skin lesions of BALB/c and C57BL/6 mice infected intradermally for 4 weeks with either L. braziliensis or L. major.

overall_design: twenty-four ear samples were recovered from either naïve mice or mice infected with Leishmania.  For each infection, 4-5 mice were processed and the entire infected ear was recovered for RNA.  Three naïve mice for each strain (Balb/c and C57BL/6) served as controls.

first: Daniel

last: Beiting

first: Phil

last: Scott

first: Fernanda

last: Novais


title: Burkitt-like lymphoma with 11q aberration: A germinal center derived lymphoma without ID3-TCF3-CCND3 pathway deregulation


title: Transcriptomic profile of ZoeJ mycobacteriophage during various stages of growth.

status: Public on Feb 18 2019

city: Pittsburgh

first: Rebekah

last: Dedrick

address: 4249 Fifth Ave

department: Biological Sciences

institute: University of Pittsburgh

summary: The goal of this sequencing project was to measure transcription levels of ZoeJ mycobacteriophage during different stages of the lifecycle, including lysogeny.

overall_design: Total RNA was isolated from cultures grown in log phase, depleted of rRNA and prepared for sequencing using a strand-specific library kit during lysogeny, and after 30min, 90min, 150min and 210min of infection by phage ZoeJ.

first: Graham

last: Hatfull

first: Rebecca

middle: A

last: Garlena


title: Nucleosomes stabilize ssRNA-dsDNA triple helices in human cells

city: Regensburg

first: Uwe

last: Schwartz

address: Universitätstraße 32

department: NGS Analysis Center

institute: University of Regensburg

summary: The molecular mechanism for ssRNA+dsDNA triple helix structure formation on chromatin are unclear. We analyzed the triplex-nucleosomes complex fomration in vitro and in vivo, and show that triplexes are stabilized by the nucleosomes. We developed a method to monitor nucleosome bound RNA triplexes in vivo, revealing that RNA binding maintained the nucleosomes on an accessible structure supporting a gene activating role of nucleosome-triplex complexes in cells.

overall_design: DNAse I digestion of chromatin to obtain mono-nucleosome from HeLa nuclei purified using the REAP method.

first: Rodrigo

last: Maldonado

first: Elisabeth

last: Silberhorn

first: Gernot

last: Längst


title: Genes activated in an SREBP1 dependent manner in ovarian cancer cells exposed to serum starvation and hypoxia

status: Public on Feb 15 2019

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

summary: To identify genes activated under serum starvation and hypoxia condition in an SREBP1 dependent manner, we performed cDNA microarray analysis with an ovarian cancer cell line OVSAYO.

overall_design: Cells were transfected with nonspecific (NS)- or SREBP1 specific-siRNA and cultured for 30 h under normoxia with 10% fetal calf serum. Cells were further cultured without serum for 16 h under normoxia and 1% O2. Total RNA was isolated for cDNA microarray analysis.

first: Shiro

last: Koizume


title: Gene Level Expression Profiling in neutrophil cells transfected with scrambled control or hsa-miR-182-5p mimic

status: Public on Feb 16 2019

city: Kaohsiung

first: Sung-Chou

last: Li

state: Kaohsiung

address: No.386, Dazhong 1st Rd

department: Department of Medical Education and Research

country: Taiwan

institute: Kaohsiung Veterans General Hospital

summary:
Transcriptome analysis of RNA samples from neutrophil cells
The RNA samples from neutrophil cells were extracted, followed by sample preparation and microarray experiment.

overall_design:
We analyzed 2 control RNA samples, 2 treatment RNA samples

contributor: Kaohsiung Chang Gung Memorial Hospital, Taiwan


title: Burkitt-like lymphoma with 11q aberration: A germinal center derived lymphoma without ID3-TCF3-CCND3 pathway deregulation [CYTOSCAN]

first: Joan

last: Ramiz-Zaldivar

overall_design:
The aim of this study was to perform a complete genetic characterization of Burkitt like lymphoma with 11q aberration. Eleven cases (8 males and 3 females; mean age: 15 years, range 8-37) with consensus diagnosis were analyzed by fluorescence in situ hybridization, copy number (CN) array and targeted sequencing analyses of genes associated with B-cell lymphoma pathology.
BLL11q_CYTOSCAN

last: Gonzalez-Farre


title: Global gene expression analysis of supression of mycotoxin biosyntheies by L-Thr in Fusarium graminearum.

city: Kanazawa

first: Takumi

last: Nishiuchi

address: 13-1 Takaramachi

country: Japan

institute: Kanazawa University

summary: We performed transcriptome analysis using an Agilent custom Fusarium graminearum 8X15k microarray  ver1.2 to profile the effects of L-Thr treatment in F. graminearum.

platform_organism:
Fusarium sporotrichioides
Fusarium graminearum

overall_design: Four condition experiments. L-Thr treated vs non-treated mycellium of F. graminearum.  Mycellium were collected at 36 or 72 hrs after L-Thr or non-treatment. Two biological replicates.

first: Makoto

last: Kimura


title: Analysis of RNA profiles in parent and Selective Inhibitors of Nuclear Export (SINE) resistant ovarian cancer cells

status: Public on Feb 14 2019

city: Okayama

first: Takahito

last: Miyake

address: 369-8 Ofuku, Minami-ku

institute: Miyake Clinic

summary: To determine the mechanism of SINE resistance, we compared RNA expression between parental and SINE resistant ovarian cancer cells.

overall_design: Parental and SINE resistant ovarian cancer cells were cultured with SINE for 24 hours, then separated and analyzed RNA profiles.

first: Anil

last: Sood


title: The role of mirna-146b-tbc1d14 in the autophagy of RAW264.7 cells mediated by b. melitensis m5-90 [miRNA]

city: shanghai

first: Xie

last: qin

address: Minchi first road, pujiang town, minhang district, Shanghai

institute: LC sciences

summary: We used B. melitensis M5-90 wild type to construct gene-deleted strains of B. melitensis ∆per, RAW264.7 cells infected with B. melitensis M5-90 and B. melitensis M5-90 ∆per for 4h, respectively. miRNA microarray and mRNA array experiments were performed, qRT-PCR validation for miRNAs and mRNAs. We performed a joint analysis of differentially expressed miRNAs and mRNAs, and proved that the target gene of miRNA-146b is Tbc1d14. It further confirmed that miR-146b targeting tbc1d14 regulates brucella-mediated autophagy of RAW264.7 cells. Finally, the molecular mechanism of tbc1d14 influencing brucella-mediated autophagy of RAW264.7 cells was preliminarily revealed by DGE sequencing.

overall_design: In this study，We used B. melitensis M5-90 wild type to construct gene-deleted strains of B. melitensis ∆per, RAW264.7 cells infected with B. melitensis M5-90 and B. melitensis M5-90 ∆per for 4h, respectively. Three samples from each of the two groups were selected for the miRNA microarray.

first: Hanwei

last: Jiao


title: RNA-seq analysis of the stem of wild type and γVPE transcriptomes

city: Beijing

first: ziyi

last: cheng

address: Tsinghua East Road 35, Haidian District

institute: Beijing Forestry University

summary: RNA-seq was performed to examine the differential expressed transcriptomes in γVPE plants during stem development compare to wild type plants.

overall_design: To examine the differential expressed transcriptomes in γVPE plants during stem development, the stem from γVPE mutants and wild type plants at 42-days after flowering were collected for RNA-seq analysis. No replicates include in each samples.

first: Ziyi

last: Cheng


title: Gene Expression Atlas of Embryo Development in Arabidopsis

city: Saskatoon

first: Peng

last: Gao

state: Saskatchewan

address: 107 Science Place

institute: Agriculture and Agri-Food Canada

summary: We combine an optimized method for isolating developing Arabidopsis embryos with high-throughput RNA-seq, to perform a bioinformatic analysis of the transcriptomic landscapes associated with embryogenesis.

overall_design: RNA-seq of Arabidopsis embryo from seven different stages.

first: Raju

last: Datla


title: Human induced pluripotent stem cell-derived hepatic stellate-like cells (iPS-HSCs) overexpressing LHX2 vs control iPS-HSCs

summary: Transcriptional profiling of human iPS-HSCs overexpressing LHX2 compared with control iPS-HSCs, which were cocultured with human induced pluripotent stem cell-derived hepatic progenitor cells (iPS-HPCs).

overall_design: Two-condition experiment, iPS-HSCs treated with doxycyclin (Dox) vs. iPS-HSCs treated with vehicle. Human iPS cell lines overexpressing LHX2 (iLHX2-iPS cells) were established. Activation of LHX2 expression in iLHX2-iPS cells is responsive to a Dox treatment. Human iPS-HSCs were induced as described as below. Human iPS-HSCs were cocultured with human iPS-derived hepatic progenitor cells for 7 days with or wihtout Dox. Harvested celles were dissociated, and were sorted using fluorescence-activated cell sorter.

first: Masato

last: Miyoshi

first: Sei

last: Kakinuma


title: Expression data from 4T1 cells in low density (LD = 2 mg/mL) or high density (HD = 3.5 mg/mL) collagen gels

first: Patricia

last: Keely

state: Wisconsin

address: 1111 Highland Ave

country: USA

institute: University of Wisconsin-Madison

summary:
The extracellular matrix has been shown to control breast epithelial cell morphogenesis, proliferation and signalling. Here we compared changes in gene expression
between 4T1 murine mammary carcinoma cells grown in a low or high density collagen matrix

overall_design: 50,000 4T1 cells were cultured in LD (2 mg/mL) or HD (3.5 mg/mL) collagen gels for 5 days before RNA extraction and hybridization on Affymetrix MTA 1.0 chips

first: Suzanne

last: Ponik

first: Brett

last: Morris

first: Brian

last: Burkel


title: TCR and BCR loci copy number aberration detection for FFPE tissues using MIP-based assay

city: Singapore

first: Siok-Bian

last: Ng

address: National University Hospital, 5 Lower Kent Ridge Road, Main Building, level 3

department: Department of Pathology

country: Singapore

institute: National University Health System, Singapore

summary:
The classification of haematolymphoid neoplasms has important clinical implications, yet current methods to determine cell lineage on formalin-fixed paraffin-embedded (FFPE) tissues are unsatisfactory, especially for neoplasms of NK- and T-cell lineages. Herein, we performed copy number analysis using the MIP platform on 86 cases, including T-, NK- and B-cell lymphomas, malignant cell lines and normal lymphocyte subsets.
We demonstrate that the loss of T- and B-cell receptor gene loci correlates with cell lineage. The overall sensitivity of the assay in our cohort was 91% and 78%, while the specificity was 84% and 93%, for the corresponding antigen receptors in T- and B-cell samples, respectively. Fluorescence in situ hybridization showed no detectable translocation or deletion of the TCRA locus in samples showing loss of TCRA. Compared to PCR-based gene arrangement assay for lineage assignment, the MIP assay showed good reliability on FFPE samples, including cases more than 10 years old. In conclusion, the detection of the loss of the antigen receptor gene loci using the MIP array is a novel genetic marker of lymphoid cell lineage and a potentially valuable tool in the diagnosis and classification of lymphoid neoplasms especially of T- and NK-cell origin.

overall_design: Comparison of T-, B- and NK-cells of diverse diseases with reference.

first: Siok

first: Tae

last: Chung


title: Transcriptional analyses of the Erythrobacter litoralis DSM 8509 general stress response system

city: East Lansing

first: Sean

last: Crosson

state: Michigan

address: 567 Wilson Rd

department: Dept. Microbiology and Molecular Genetics

institute: Michigan State University

summary: We measured steady-state transcript levels in 1) wild-type E. litoralis DSM 8509, 2) a nepR-ecfG deletion strain (ΔnepR-ecfG), 3) a phyR deletion strain (ΔphyR), 4) a lovK-lovR deletion strain (ΔlovKR), and 5) a gsrK-gsrP deletion strain (ΔgsrKΔgsrP) cultivated in constant white light or in constant dark conditions.

overall_design: Cultures of Erythrobacter litoralis DSM 8509 wild-type and mutant strains were grown in 0.5x marine broth in the presence or absence of white light.

first: Aretha

last: Fiebig


title: The role of mirna-146b-tbc1d14 in the autophagy of RAW264.7 cells mediated by B. melitensis m5-90

first: Xie

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

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

overall_design: Refer to individual Series


title: Genome-wide DNA methylation profiling shows a distinct epigenetic signature associated with lung macrophages in cystic fibrosis

city: Lebanon

first: Youdinghuan

last: Chen

state: NH

address: Hinman Box 7650

department: Epidemiology

institute: Dartmouth College

summary: Lung macrophages are major participants in the pulmonary innate immune response. In the cystic fibrosis (CF) lung, the inability of lung macrophages to successfully regulate the exaggerated inflammatory response suggests dysfunctional innate immune cell function. In this study, we aim to gain insight into innate immune cell dysfunction in CF by investigating alterations in DNA methylation in bronchoalveolar lavage (BAL) cells, composed primarily of lung macrophages of CF subjects compared with healthy controls. All analyses were performed using primary alveolar macrophages from human subjects collected via bronchoalveolar lavage. Epigenome-wide DNA methylation was examined via Illumina MethylationEPIC (850 K) array. Targeted next-generation bisulfite sequencing was used to validate selected differentially methylated CpGs. Methylation-based sample classification was performed using the recursively partitioned mixture model (RPMM) and was tested against sample case-control status. Differentially methylated loci were identified by fitting linear models with adjustment of age, sex, estimated cell type proportions, and repeat measurement.

overall_design: Bronchoalveolar Lavage (BAL) samples were sequentially collected from the lung right upper lobe (RUL) and right lower lobe (RLL) of 4 cystic fibrosis (CF) and 4 healthy (H) control subjects. 2 samples from each subject were then measured on the MethylationEPIC array

first: David

last: Armstrong


title: Characterization of tumor-infiltrating T cells by TCR-β repertoire analyses

status: Public on Feb 13 2019

city: Chiyoda

first: Ranmaru

last: Shimoda

state: Tokyo

address: 3F Yayoi Bldg., 3-7-4 Iwamotocho

institute: Rhelixa, Inc.

summary: Local administration of IFN-α-producing proliferating myeloid cells (IFN-α-iPSC-pMCs) inhibited the tumor growth not only at the treatment site but also at the distant site (left). T cell receptor (TCR)-β chain repertoire and complementarity determining region 3 (CDR3) gene sequence analyses of tumor-infiltrating lymphocytes (TILs) showed marked enrichment of T cells with identical TCR-β chains in bilateral tumor tissues.

overall_design: TCR-β repertoire analyses of IFN-α-iPSC-pMC-treated tumor, distant tumor, and spleen (2 mice)

first: Y

last: Uemura

first: R

last: Zhang


title: The lineage-specific transcriptional regulator, CDX2, navigates a dynamic chromatin landscape to control distinct stages of intestinal development

city: Piscataway

first: Michael

last: Verzi

state: NJ

address: 145 Bevier Road

department: Genetics

institute: Rutgers, the State University of New Jersey

summary: Important lineage regulators, such as the intestinal lineage regulator CDX2, can function over the timespan of intestinal development. The consequences of CDX2 knockout in the embryo versus in the adult are quite distinct. The data below provide a rationale for these divergent transcription factor functions in distinct developmental contexts, with unique binding patterns of CDX2 observed via ChIP-seq and unique gene regulatory targets defined via RNA-seq. The dynamic gene regulatory program controlled by CDX2 is conserved in mice and humans.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: CDX2 ChIP-seq and RNA-seq experiments were conducted at various stages of mouse or human iPSC-derived tissues or primary adult human tissues.

first: Namit

last: Kumar

first: Lei


title: The phase-shifting effect of bright light exposure on circadian rhythmicity in the human transcriptome

city: Montreal

first: Laura

last: Kervezee

state: Quebec

address: 6875 LaSalle Boulevard

department: Douglas Mental Health University Institute

institute: McGill University

summary: Eleven healthy human subjects were enrolled in a 6-day simulated shift work protocol. Blood samples were collected during the two 24-hour measurement periods. Blood samples were collected every 4 hours during both measurement periods. Subjects entered the lab on Day 1. At the start of Day 2, the first 24-hour measurement period was started. Subjects slept according to their habitual sleep/wake schedule, followed by a 16-hour constant posture procedure. On days 3-6, the sleep period was delayed by 10 hours. Participants in the control group were exposed to dim light throughout the waking periods; participants in the bright group were exposed to bright light (~6,000lux) for 8 hours during the waking period. Following the third night on this schedule, subjects underwent another 24-hour measurement period. During both measurement periods, blood samples were collected and PBMCs were isolated. mRNA was extracted, labelled, and hybridized to microarrays.

overall_design: A total of 141 samples were collected from 11 subjects spread across two 24-hour measurement periods

first: L

first: M

last: Cuesta

first: N

last: Cermakian

first: D

last: Boivin


title: Gene expression analysis of a subcutaneous MV4;11 tumor treated with curaxin CBL0137.

city: Randwick

first: Michelle

last: Haber

state: NSW

address: Lowy Cancer Research Centre, PO BOX 81

country: Australia

institute: Children's Cancer Institute

summary: The aim of this experiment was to identify how CBL0137 decreased tumor growth in a subcutaneous MV4;11 xenograft model by investigating the gene expression changes induced upon treatment.

overall_design: > 1 million MV4;11 cells were inoculated subcutaneously in the flank of NOD/SCID (NOD/SCID NOD.CB17-Prkdcscid/SzJ) mice. When tumors measured around 100 mm3, mice were treated with CBL0137 (70 mg/kg CBL0137 intravenously) on day 0 and day 8. Tumors were harvested 24h post last injection on day 8. Tumors were also harvested from untreated mice. Tumors were flash frozen in liquid nitrogen and RNA was isolated.

first: Katerina

middle: V

last: Gurova

first: Nikolay

last: Neznanov

first: Chelsea

last: Mayoh

first: Klaartje

last: Somers

middle: J

last: Henderson


title: Prediction for the development of new distant metastases using serum microRNAs in patients with metastatic breast cancer treated with eribulin

first: Ichikawa

last: Makiko

institute: Toray Industries, Inc.

summary: The combination of serum miRNAs could be a classifier for predicting the development of new distant metastasis in breast cancer patients during the treatment of eribulin

overall_design: Serum microRNA profiles and clinical characteristics of 147 woman with breast cancer

first: Natsuko

last: Tsushita

first: Akihiko

last: Shimomura

first: Juntaro

last: Matsuzaki

first: Junpei

last: Kawauchi

first: Satoko

last: Takizawa

first: Yoshiaki

last: Aoki

first: Hiromi

last: Sakamoto

first: Chikako

last: Shimizu

first: Kenji

last: Tamura

first: Takahiro

last: Ochiya


title: Spatial and temporal heterogeneity of mouse and human microglia at single-cell resolution

city: Freiburg

first: Sagar

address: Hugstetter Straße 55

department: Department of Internal Medicine II

country: Germany

institute: University Medical Center Freiburg

summary: Microglia play critical roles in neural development and homeostasis. They are also implicated in neurodegenerative and neuroinflammatory diseases of the central nervous system (CNS). However, little is known about the presence of spatially and temporally restricted subclasses of microglia during CNS development and disease. Here, we combined massively parallel single-cell analysis, single-molecule FISH, advanced immunohistochemistry and computational modelling to comprehensively characterize novel microglia subclasses, which were transcriptionally different from perivascular macrophages, in up to six different CNS regions during development and diseases. Single-cell analysis revealed specific time- and region-dependent microglia subtypes during homeostasis. In contrast, demyelinating and neurodegenerative diseases evoked context-dependent microglia subtypes with distinct molecular hallmarks and diverse cellular kinetics. Finally, diverse microglia subsets were also identified in normal and diseased human brains. Our data provide new insights into the CNS endogenous immune system during development, health and perturbations.

overall_design: CD45+ cells isolated from healthy and MS-affected human brains were FACS-sorted in 384-well plates and used for scRNAseq. The patients were aged between 22 and 25 years. Data comprises 5 healthy and 5 MS patients. CEL-Seq2 protocol was used for single cell sequencing (Hashimshony et al. 2016).

last: Masuda

first: Roman

last: Sankowski

first: Ori

last: Staszewski

last: Sagar

first: Dominic

last: Gruen

first: Marco

last: Prinz


title: Effect of GLUT1 deletion in myeloid deficient bone marrow derived macrophage LysM-Cre X Slc2a1 model

city: Memphis

first: Liza

last: Makowski

state: Tennessee

address: 19 South Manassas St

department: Medicine- Heme Onc

institute: UTHSC

summary:
Macrophages (MΦs) are heterogeneous and metabolically flexible with metabolism strongly affecting immune activation. A classic response to pro-inflammatory activation is increased flux through glycolysis with a downregulation of oxidative metabolism, while alternative activation is primarily oxidative which begs the question of whether targeting glucose metabolism is a viable approach to control MΦ activation. We created a murine model of myeloid-specific glucose transporter GLUT1 (Slc2a1) deletion. Bone marrow derived MΦs (BMDM) from Slc2a1M-/- mice failed to uptake glucose and demonstrated reduced glycolysis and Pentose Phosphate Pathway activity. Activated BMDMs displayed elevated metabolism of oleate and glutamine, yet maximal respiratory capacity was blunted in MΦ lacking GLUT1 demonstrating an incomplete metabolic reprogramming. Slc2a1M-/- BMDMs displayed a mixed inflammatory phenotype with reductions of the classically-activated pro- and anti-inflammatory markers, yet less oxidative stress. Slc2a1M-/- BMDMs had reduced pro-inflammatory metabolites, whereas metabolites indicative of alternative activation - such as ornithine and polyamines - were greatly elevated in the absence of GLUT1. Adipose tissue MΦs of lean Slc2a1M-/- mice had increased alternative M2-like activation marker mannose receptor CD206, yet lack of GLUT1 was not a critical mediator in the development of obesity-associated metabolic dysregulation. However, Ldlr-/- mice lacking myeloid GLUT1 developed unstable atherosclerotic lesions. Defective phagocytic capacity in Slc2a1M-/- BMDMs may have contributed to unstable atheroma formation. Together our findings suggest that while lack of GLUT1 blunted glycolysis and PPP, MΦ were metabolically flexible enough that inflammatory cytokine release was not dramatically regulated yet phagocytic defects hindered MΦ function in chronic diseases.
Control mice are noted as WT or Slc2a1 fl/fl and myeloid GLUT1 deficient are KO or Slc2a1M-/- (LysMCre X Slc2a1fl/fl) for myeloid deficiency.

overall_design: Gene expression was measured in 4 biological replicates for each of three BMDM activation states (unstimulated M0, LPS/IFNg M1, and IL4 M2) from both Slc2a1M-/- and Slc2a1 fl/fl mice.

first: Alex

last: Freemerman


title: EphB2-dependent signaling promotes neuronal excitotoxicity and inflammation in the acute phase of ischemic stroke

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary: Local cerebral hypoperfusion causes ischemic stroke while driving multiple cell-specific responses including inflammation, glutamate-NMDAR-mediated neurotoxicity, edema formation and angiogenesis. Despite the relevance of these pathophysiological mechanisms for disease progression and outcome, molecular determinants controlling the onset of these processes are only partially understood. In this context, our study intended to investigate the functional role of EphB2 – a receptor tyrosine kinase that is crucial for synapse function and binds to membrane-associated ephrin-B ligands.  Cerebral ischemia was induced in EphB2-deficient mice by transient middle cerebral artery occlusion followed by different times (6, 12, 24 and 48 h) of reperfusion. Histological, neurofunctional and transcriptome analyses indicated an increase in EphB2 phosphorylation under these conditions and attenuated progression of stroke in EphB2-deficient mice. Moreover, while infiltration of microglia/macrophages and astrocytes into the peri-infarct region was not altered, expression of the pro-inflammatory mediators MCP-1 or IL-6 was decreased in these mice. In fact, in vitro analyses indicated that binding of EphB2 to astrocytic ephrin-B ligands stimulates NF-κB-mediated cytokine expression via the MAPK pathway. Further magnetic resonance imaging of the EphB2-deficient ischemic brain revealed a lower level of neuronal cytotoxic edema formation within 6 h upon onset of reperfusion. On the mechanistic level, absence of neuronal EphB2 decreased the mitochondrial Ca2+ load upon activation of NMDAR but not AMPAR. Moreover, activation of EphB2 by ephrin-B2 enhanced the NMDA-evoked excitotoxic neuronal cell death in vitro while neuron-specific loss of ephrin-B2 reduced the extent of cerebral tissue damage in the acute phase of ischemic stroke.  Collectively, EphB2 may promote the immediate response to an ischemia-reperfusion event in the central nervous system by (i) pro-inflammatory activation of astrocytes via ephrin-B-dependent signalling and (ii) amplification of the NMDA-evoked neuronal excitotoxicity.

overall_design: 3 WT and 3 Ephb2-KO mice (with a C57Bl/6 background.) were subjected to 60 min MCAo followed by 48 h of reperfusion. Brains were harvested. Bulbi and cerebellum were removed, brains were separated into hemispheres (ipsilateral=ischemic and contralateral=normoxic control). RNA was extracted from tissue for hybridization on Affymetrix microarrays. We aimed at identifying (1) genes and gene sets that are up- or down-regulated upon ischemia by comparison of ipsi- and contralateral hemispheres of the same genotype, (2) genes and gene sets that are differentially regulated between the two genotypes upon ischemia by comparison of the ipsilateral hemispheres, and (3) genes and gene sets that are differentially regulated between the two genotypes at basal levels by comparison of the contralateral hemispheres.

first: Anne-Sophie

last: Ernst

first: Laura-Inés

last: Böhler


title: Genome-wide identification of microRNAs in response to salt/alkali stress in Medicago truncatula through high-throughput sequencing

first: Ruicai

last: Long

address: No. 2 Yuanmingyuan west road, Haidian, Beijing

country: China

institute: Institute of Animal Sciences, Chinese Academy fo Agricultral Sciences

summary: The miRNA contained in the total RNA extracted from Medicago truncatula seedlings (72 hours) that had been treated with solutions mimicking saline and alkaline soils was subjected to miRNA deep sequencing. Sequencing revealed that 876 miRNAs including 664 known miRNAs and 212 potential novel miRNAs were present in all the libraries.

overall_design: Examination of Medicago truncatula seedlings treated with salt and alkali.

first: Chunyu

last: Cao


title: PARP inhibition elicits STING-dependent antitumor immune responses in Brca1-deficient ovarian cancer

city: Boston

first: Jean

last: Zhao

state: MA

address: 450 Brookline Ave

department: Cancer Biology

institute: Dana-Farber Cancer Institute

summary: To examine the immune responses that occur in Brca1-deficent tumors upon olaparib treatment, we performed gene expression analysis of a panel of 4604 cancer and immune-related genes in tumor tissues harvested from Brca1-deficient ovarian tumor-bearing mice after treatment with olaparib or vehicle. Transcriptome analysis showed that the expression of genes associated with immune response, T-cell activation and interferon-gamma(IFNgamma) response were markedly upregulated in tumors treated with olaparib as compared to vehicle.  Our data reveal the antitumor immune response  of PARP inhibition and demonstrate that it contributes to therapeutic efficacy of PARP inhibition in Brca1-deficient tumors.

overall_design: Transcriptome analysis were performed on bulk tumors collected from Brca1-deficient ovarian tumor bearimg mice treated with olaparib or vehicle control.

first: Liya

last: Ding