title: Distinct mesenchymal lineages and niches promote epithelial self-renewal and myofibrogenesis in the lung [Single cell RNA-Seq]

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

summary: Single cell RNAseq using the 10x gemcode platform on bulk mesenchyme from one adult 6w old mouse.

overall_design: Lungs were harvested from a 6-week old adult mouse and digested to generate a single-cell suspension. The cell suspension was stained with antibodies directed against Epcam, CD31 and CD45. DAPI was included as a live/dead stain. Cells that were negative for DAPI, EPCAM, CD31 and CD45, were sorted into collection buffer. The purified cells, referred to as bulk mesenchyme, were manually counted and subsequently loaded onto the 10x Genomics instrument, libraries were prepared according to the manufacture's protocol.

first: Jarod

last: Zepp

first: Edward

last: Morrisey


title: Physical exercise on proteoglycan_induced arthritis (PGIA) mice_transcriptome responses on tarsal joint

status: Public on Sep 12 2017

city: Chihuahua

first: Susana

middle: Aideé

last: González-Chávez

state: Chihuahua

address: Circuito Universitario Campus II

department: Facultad de Medicina

country: Mexico

institute: Universidad Autónoma de Chihuahua

summary: Gene expression profiles in the tarsal bones and joints of mice that performed treadmill exercise vs. those who were not exercised were compared. Exercise induced the downregulation of genes and signaling pathways that mediates and promotes the inflammatory process and triggered the upregulation of genes associated to cartilage remodeling and bone mineralization.

overall_design:
Pools of total RNA were made per study group (seven mouse per group): PGIA exercised mice (test group) and PGIA non-exercised mice (reference). The reverse transcription polymerase chain reaction (RT-PCR) was performed and the resulting complementary DNAs were labeled with Alexa547 (PGIA exercised mice) or Alexa555 (PGIA non-exercised mice). Hybridation analysis used the mouse 65-mer oligo library from Sigma-Genosys to compare the expression of 23,232 gene-specific oligonucleotide probes for mouse.

The '2_M22K_09_24.xlsx' contains the raw data;
the '3_M22K_09_24_normalized.xlsx' contains the normalized and background data for each channel (prior to generating the ratio data)

Please note that AIPG (in the sample title) corresponds to PGIA (proteoglycan_induced arthritis) in the Series title

middle: A

first: César

last: Pacheco-Tena

first: Celia

middle: M

last: Quiñonez-Flores


title: Comparison of DNA methylomes of human monocyte-derived dendritic cells (DCs) and myeloid-derived suppressor cells (MDSCs) generated in co-culture with ovarian carcinoma cell line (OVCAR8) during 6 days

status: Public on Sep 11 2017

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Josep Carreras Research Institute (IJC)

type: Methylation profiling by genome tiling array

summary: The methylation profiles of bisulfite-modified DNA of human CD14+ monocytes-derived immature dendritic cells (GM-CSF/IL-4) were compared with myeloid-derived suppressor cells (GM-CSF/IL-4 in co-culture with ovarian carcinoma cell line (OVCAR8)) using the Infinium HumanMethylation450 BeadChips (Illumina, Inc., San Diego, CA). This platform allows the interrogation of >485,000 methylation sites per sample at single-nucleotide resolution, and comprises an average of 17 CpG sites per gene in the 99% of RefSeq genes. 96% of CpG islands are covered, with additional coverage in CpG island shores and the regions flanking them. The samples were hybridized in the array following the manufacturer’s instructions.

overall_design: Total DNA isolated by standard procedures from three sets of samples of derived immature dendritic cells (DCs) and myeloid-derived suppressor cells (MDSCs).

first: Javier

last: Rodríguez-Ubreva

first: Francesc

last: Català-Moll

first: Natasa

last: Obermajer

first: Damiana

last: Álvarez-Errico

first: Ricardo

middle: N

last: Ramirez

first: Carlos

last: Company

first: Roser

last: Vento-Tormo

first: Gema

last: Moreno-Bueno

first: Robert

middle: P

last: Edwards

first: Ali

last: Mortazavi

first: Pawel

last: Kalinski


title: Sequencing of tumor associated (B16f10-OVA) mir-155 Wt or deficient CD4+ and CD8+ T cells

city: Salt Lake City

first: Ryan

last: O'Connell

state: UT

address: 15 N Medical Dr.

country: USA

institute: University of Utah

type: Expression profiling by high throughput sequencing

summary: Tumor associated CD4+ and CD8+ T cells were sorted from B16f10 OVA expressing tumors in miR-155 flox, miR-155 flox CD4Cre+, and miR-155 flox CD4Cre+ mice treated with immune checkpoint blocking (ICB) antibodies by flow sorting on CD45+CD3+CD4+ cells and CD45+ CD3+CD8+ cells. RNA was collected from these cells to perform RNA sequencing of total RNA.

overall_design: Each sample represents cells from 2  to 3 individual tumors grown on individual mice that were pooled together before sorting via flow cytometry

first: Thomas

middle: B

last: Huffaker


title: Comparison of the RNA expression profiles of CD14+ monocytes from human peripheral blood with derived dendritic cells (DCs) and myeloid-derived suppressor cells (MDSCs) obtained by exposure with GM-CSF/IL4 and GM-CSF/IL4/PGE2, respectively, during 6 days

summary: The expression profiles of RNA of human CD14+ monocytes were compared with derived dendritic cells (DCs) and myeloid-derived suppressor cells (MDSCs) following GM-CSF/IL4 and GM-CSF/IL4/PGE2 incubation for 6 days using the Agilent Human GE v3 8x60K array (Agilent Technologies, CA, USA). The samples were hybridized in the array following the manufacturer’s instructions.

overall_design: Total RNA isolated by standard procedures from CD14+ cells (total monocytes, MOs) corresponding to three sets of samples of monocytes (MOs) and derived DCs and MDSCs following incubation with GM-CSF/IL4 and GM-CSF/IL4/PGE2, respectively, for 6 days.


title: Expression data from rodents following ischemic injury, permanent middle cerebral artery occlusion (MCAO) Neuregulin-1 treatment.

status: Public on Sep 09 2017

city: Riverside

first: Byron

last: Ford

state: CA

address: 0207 School of Medicine Research Building

institute: University of California,Riverside

summary: We used gene expression profiling to understand the cellular and molecular mechanisms of NRG1’s effects 3 hours after the induction of ischemia.

overall_design: Cortical brain tissues were collected three hours following MCAO and NRG1 treatment, RNA extracted and hybrdized to an Affymetrix microarray chip.

first: Monique

last: Surles-Zeigler

first: Yonggang

last: Li


title: Transcriptome data of Pichia caribbica induced by H2O2

status: Public on Sep 10 2017

city: Zhenjiang

first: Xiangfeng

last: Zheng

state: Jiangsu

address: 301, Xuefu Road

department: Food school

country: China

institute: Jiangsu university

summary: Pichia caribbica, which was isolated by our laboratory, was cultured at 4 °C on nutrient yeast dextrose agar (NYDA).A loop of the culture was inoculated in nutrient yeast dextrose broth and incubated on a rotary shaker at 180 rpm at 28 °C for 20 h.

overall_design: Pichia caribbica cultured at NYDB (control, non H2O2) and NYDB ( induced by H2O2)

first: Hongyin

last: Zhang

first: Junwei

last: Diao


title: Gene expression data from irradiated mouse liver

city: Busan

first: Sungmin

last: Lee

address: 2, Busandaehak-ro 63 beon-gil

department: Integrated Biological Science

country: South Korea

institute: Pusan National University

summary:
In previous studies, it was observed that survivors who received stem cell transplantation and whole body irradiation showed development of NAFLD as a chronic effect.
To elucidate the molecular mechanism of radiation-induced NAFLD, we conducted transcriptoic analysis in mice which received whole body irradiation and developed NAFLD.

overall_design: The 4-week-old C57BL/6 mice were treated with 6 Gy of single gamma-ray and incubated for 5 weeks. Total RNA was isolated from liver tissue and subjected to microarray

first: Beomseok

last: Son

first: Jaewan

last: Jeon

first: Gaeul

last: Park

first: Hyunwoo

last: Kim

first: Hyunkoo

last: Kang

first: HyeSook

last: Youn

first: Sunmi

last: Jo

first: Jie-Young

last: Song

first: BuHyun


title: Distinct cell cycle control in naïve and primed mouse pluripotency [ChIP-seq]

status: Public on Sep 13 2017

city: Nijmegen

first: Menno

last: ter Huurne

address: Geert Grooteplein 26

department: Molecular Biology

country: Netherlands

institute: Radboud University Nijmegen

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The cell cycle of primed pluripotent mouse serum ESCs is characterised by a shortened G1-phase. Here we assessed the differences in cell cycle between serum ESCs and naive 2i ESCs.

overall_design: Mouse ESCs were cultured either in serum conditions or 2i conditions. Cells were fixed chromatin was extracted. Biological replicate included.

first: Henk

last: Stunnenberg


title: Growth factor-free, chemically-defined culture system for expansion and derivation of human pluripotent stem cells

city: Suita

first: Kouichi

last: Hasegawa

state: Osaka

address: 6F Techno Alliance Bldg. 2-8 Yamadaoka

department: StemRIM Institute of Regeneration-Inducing Medicine

country: Japan

institute: Osaka University

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

overall_design: Refer to individual Series


title: Transcriptional alterations in mDia1-miR146a double deficient erythroblasts and  IL-6 treated erythroblasts

city: Chicago

first: Peng

last: Ji

state: IL

address: 303 E. Chicago Ave

department: Pathology

institute: Northwestern University

summary:
Transcriptome analysis of total RNA samples from FACS sorted erythroblasts
To further verify the role of cytokine triggered inflammation signaling in erythropoiesis, we decided to follow the profile of gene expression in erythroblasts using DNA microarrays. To elucidated the gene expression pattern in cytokine, especially IL-6, challenged erythroblasts, in vitro IL-6 treated erythroblasts in EPO containing medium both at day 1 and day 2 were collected. We also sorted the erythroblasts at different stages (Proerythroblasts(I),Basophilic(II) and polychromatic(III) erythroblasts,Orthochromatic(IV) erythroblasts) from both DWT and DKO bone marrow cells through fluorescence activated cell sorting. Total RNA were extracted and processed to hybridize with Affymetrix mouse Clariom S microarrays.

overall_design: We analyzed erythroblasts at different stages from 2 double WT and 2 mDia1-miR-146a double KO old mice in C57BL/6 background using the affymetrix Mouse Clariom S Array platform. In vitro IL-6 treated and non-treated erythroblasts differentiated from two wide type C57BL/6 mice were also inclued.No techinical replicates were performed.

first: Yang

last: Mei


title: C-reactive protein promotes bone destruction in human myeloma by stimulating myeloma cell production of osteolytic cytokines via the CD32A-p38MAPK-twist axis

city: Houston

first: Jing

last: Yang

state: Texas

address: 7455 Fannin

institute: MD Anderson Cancer Center

summary: Bone destruction is a hallmark of human myeloma and affects more than 80% of patients. Although it is well established that myeloma cells mediate bone destruction by activating osteoclasts, the mechanism how myeloma cells are regulated to do so is unknown. Here we show that C-reactive protein (CRP), a protein secreted in elevated amounts by hepatocytes in response to myeloma-derived cytokines, may be responsible for activating myeloma cells to promote osteoclastogenesis and inducing bone destruction in vivo. CRP binds to surface CD32A/FcRIIA, activates p38MAPK-twist pathways, and upregulates the secretion of osteolytic cytokines by myeloma cells. Clinical studies examining the relationship between the levels of serum CRP and the numbers of osteolytic bone lesions in newly diagnosed patients support this conclusion.

overall_design: Three different human myeloma cell lines (ARP-1, MM.1S and U266) were treated with or without 5 ug/ml CRP for 24 hours. Then total RNA for myeloma cell lines or myeloma cell lines treated with CRP was extracted and used for comparison by gene expression profiling.

first: Zhiqiang

last: Liu

first: Huan

first: Jin

last: He

first: Jianling

first: Pei

last: Lin

first: Qiang

last: Wang

first: Juan

last: Du

first: Wencai

last: Ma

first: Eric

last: Davis

first: Robert

middle: Z

last: Orlowski

first: Jian

last: Hou

first: Qing

last: Yi


title: Human embryonic stem cells in AKIT, E8 and KSR/bFGF culture medium

status: Public on Sep 08 2017

summary:
Analysis of KhES-1 and H9 human ES cells in growth factors-dependent (E8) and -independent (AKIT) medium in feeder-free culture condition and KSR/bFGF medium on a feeder-layer.
Results provide insight into genetic stability in different culture media/conditions.

overall_design: CNV and LOH analysis of KhES-1 and H9 human ES cells maintained in AKIT and E8 feeder-free culture, and KSR/bFGF on feeder culture.

first: Tatsuhiko

last: Ikeda

first: Shinys

last: Yasuda


title: Gene expression profiling in rat liver after H2 administration with or without dietary stress

city: Kasugai

first: Masatoshi

last: Ichihara

state: Aichi

address: 1200 Matsumoto-cho

institute: Chubu University

summary: Molecular hydrogen (H2) is a biologically active gas that is used medically to ameliorate various systemic pathological conditions. H2 also regulates gene expression involved in intracellular signaling and metabolic pathways. Therefore, we attempted to identify genes that exhibit similar changes in expression in response to H2 by employing DNA microarrays and gene set enrichment analysis. We found that H2 activated the expression of sets of genes regulated by histone H3K27 methylation status. H2 also modified the expression of many genes regulated by a wide variety of signaling pathways.

overall_design: We divided 4-week-old male F344 rats into four groups: 1) control/normal diet group: fed with basal rodent chow (CE-2; CLEA Japan Inc., Tokyo, Japan) and reared in air (n = 4), 2) hydrogen-treated/normal diet group: fed with basal rodent chow and hydrogen-rich water in 2% hydrogen/98% air (n = 4), 3) control/CDAA diet group: fed with a choline-deficient L-amino acid-defined diet (CDAA diet; A06083101, Research Diets, Inc., New Brunswick, NJ) and reared in air (n = 4), 4) hydrogen-treated/CDAA diet group: fed with CDAA diet and hydrogen-rich water in 2% hydrogen/98% air (n = 4). Hydrogen-rich water (0.7mM dissolved hydrogen) was generated from distilled water with 0.44 mM Na2SO4 using Aquela Blue, a water-electrolyzing device to produce electrolyzed hydrogen-saturated water near neutral pH (MiZ Co., Ltd, Fujisawa, Japan). The control dehydrogenized water was prepared by gently stirring hydrogen-rich water in open air for 24 hours. Hydrogen-rich water or control water was administrated ad libitum to the rats with a 50-ml closed glass vessel equipped with an outlet line having a ball bearing. After 3-week rearing, the rats were sacrificed and their livers were excised for RNA extraction. Furthermore, we performed DNA microarray analysis to examine changes in the gene expression profiles.

first: Sayaka

last: Sobue


title: Gene expression profiling in mouse lung after H2 administration

overall_design: We divided 10-week male BALB/c mice into two groups: 1) control group: reared in air (n = 3), 2) hydrogen-treated group: reared in 2% hydrogen/98% air (n = 3). After 3-week rearing, the mice were sacrificed and their lungs were excised for RNA extraction. Gene expression profile was compared by microarray.


title: Molecular hydrogen modulates gene expression via histone modification and induces the mitochondrial unfolded protein response

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus


title: LncRNA expression in CD4+ T cells in neurosyphilis patients

city: Fujian

first: Li-Li

address: No.201 Hubin South Road

institute: Zhongshan Hospital, Medical College of Xiamen University

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

summary:
Objective: To analysis lncRNAs expression profiles and identify differentially expressed lncRNAs in CD4+ T cells response to T. pallidum infection in neurosyphilis patients.
Methods: CD4+ T cells were isolated from peripheral blood mononuclear cells. RNA extraction was performed to conduct further experiments. Expression profiles of mRNAs and lncRNAs in CD4+ T cells isolated from neurosyphilis patients and healthy controls were analyzed by using microarray assay. Four lncRNAs were selected to conduct validation by using real time-quantitative polymerase chain reaction and the expression levels of those above mentioned lncRNAs in neurosyphilis patients and healthy controls were compared.
Results: In total, 17, 278 lncRNAs and 15, 840 mRNA were found to be differentially expressed when comparing the CD4+ T cells between neurosyphilis patients and healthy control individuals. Of these transcripts, 2258 lncRNAs and 1728 mRNAs were significantly over or under expressed, respectively. Compared with healthy controls, AC068282.3 (fold change: 21.90) and CTD-3064M3.3 (fold change: 23.93) were the most over-expressed and under-expressed lncRNAs in neurosyphilis patients. The majority of differentially expressed lncRNAs are from intergenic regions (~ 57.5%), intronic antisense to protein-coding loci (~ 15.0%), natural antisense to protein-coding loci (~12.1%). It is worth noting that 59 lncRNAs were significant difference along with significantly different mRNA. Among the 59 pairs of genes, LOC7999 mRNA was positively correlated with lncRNA RP11-160E2.16, RP11-160E2.11, RP11-160E2.19, respectively; NKX1-1 mRNA was positively correlated with lncRNA RP11-1398P2.1, RP11-160E2.19, XLOC_003422, respectively. The following five mRNAs were correlated with two differential lncRNAs, namely DUSP16, AP000349.1, FAM115C, TIMM8A, SMCHD1. GO analysis revealed that the differentially expressed coding genes were mainly involved in the biological processes, and among them, the most significant association was observed in defense response to fungus, defense response to bacterium, killing cells of other organism and disruption of cells of other organism. Subsequent pathway analysis was also conducted, and T cell receptor signaling pathway, MAPK signaling pathway, TGF-beta signaling pathway, etc. were found out to be associated with differentially expressed mRNAs.
Conclusion: The present study revealed the differential expression profiles of lncRNAs in CD4+ T cells response to T. pallidum infection in neurosyphilis patients. LncRNAs are involved in the key biological process in CD4+ T cell response to T. pallidum infection.

overall_design: Two-condition experiment, healthy control vs. neurosyphilis. Biological replicates: 3 control replicates, 3 neurosyphilis replicates.

first: Shao-Gang

last: Zhu

first: Xiao-Yong

last: Jiang

first: Jun

last: Ren

first: Yong

first: Ning-Ning

last: Zhang

first: Man-Li

last: Tong

first: Hui-Lin

first: Wei-Hong

last: Zheng

first: Hua-Jun

last: Fu

first: Hai-Juan

last: Luo

first: Li-Rong

first: Jiang-Hua

last: Yan

first: Tian-Ci


title: First trimester human placenta prevents breast cancer cell attachment to the matrix: the role of extracellular matrix

status: Public on Sep 07 2017

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

summary: The placenta is a nonsupportive microenvironment for cancer cells. We showed that breast cancer cells (BCCL) were eliminated from placental implantation sites. During implantation, the placenta manipulates its surrounding matrix, which may induce BCCL elimination. Here, we explored the effect of placenta-induced ECM manipulations on BCCL. During experiments, BCCL (MCF-7/T47D) were cultured on placenta/BCCL-conditioned ECM (Matrigel used for first trimester placenta/BCCL culture and cleared by NH4OH). After culturing the cells, we analyzed cancer cell phenotype (death, count, aggregation, MMP) and signaling (microarray analysis and pathway validation). We found that the BCCL did not attach to previous placental implantation sites and instead, similarly to anoikis-resistant cells, migrated away, displayed increased MMP levels/activity, and formed aggregates in distant areas. T47D were less affected than the MCF-7 cells, since MCF-7 also showed modest increases in cell death, EMT, and increased proliferation. Microarray analysis of the MCF-7 highlighted changes in the integrin, estrogen, EGFR, and TGFb pathways. Indeed, placental ECM reduced ERa, induced Smad3/JNK phosphorylation and increased integrin-a5 expression (RGD-dependent integrin) in the BCCL. Addition of RGD or TGFbR/JNK inhibitors reversed the phenotypic changes. This study helps explain the absence of metastases to the placenta and why advanced cancer is found in pregnancy, and provides possible therapeutic targets for anoikis-resistant cells.

overall_design: Cells were cultured with or without placetal-conditioned extracellular matrix, and microarrays were used to estimate changes in gene expression.

first: Gali

last: Epstein Shochet

first: Liat

last: Drucker

first: Meir

last: Pomeranz

first: Ami

last: Fishman

first: Shelly

last: Tartakover-Matalon

first: Michael

last: Lishner


title: Small RNA transcriptome of Hibiscus syriacus provides insights into the potential influence of microRNAs in flower development and terpene synthesis

city: Seoul

first: Chanseok

last: Shin

address: 1, Gwanak-ro, Gwanak-gu

department: Agricultural Biotechnology

institute: Seoul National University

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNAs (miRNAs) are essential small RNA molecules that regulate the expression of target mRNAs in plants and animals. Here, we aimed to identify miRNAs and their putative targets in Hibiscus syriacus, the national flower of South Korea. Therefore, we employed high-throughput sequencing of small RNAs obtained from four different tissues (i.e., leaf, root, flower, and ovary) and identified 33 conserved and 30 novel miRNA families, many of which showed differential tissue-specific expressions. In addition, we computationally predicted novel targets of miRNAs and validated some of them using 5′ rapid amplification of cDNA ends analysis. One of the validated novel targets of miR477 was a terpene synthase, the primary gene involved in the formation of disease-resistant terpene metabolites such as sterols and phytoalexins. In addition, a predicted target of conserved miRNAs, miR396, is SHORT VEGETATIVE PHASE, which is involved in flower initiation and is duplicated in Hibiscus syriacus. Collectively, this study provides the first reliable draft of the Hibiscus syriacus miRNA transcriptome that should constitute a basis for understanding the biological roles of miRNAs in Hibiscus syriacus.

overall_design: Total RNAs were extracted from H. syriacus tissue samples (leaf, root, flower, and ovary).

first: Taewook

last: Kim

first: June

last: Park

first: Sang-gil

last: Lee

first: Soyoung

first: Jihyun

first: Jungho


title: Comparative analysis of transcriptomes from the carotid body, adrenal medulla, and superior cervical ganglion of adult mice

city: Seville

first: Lin

last: Gao

address: Avda Manuel Siurot, Hospital Virgen del Rocío

institute: Instituto de Biomedicina de Sevilla

summary:
Acute O2 sensing is a fundamental property of cells in the peripheral chemoreceptors, e.g. glomus cells in the carotid body (CB) and chromaffin cells in the adrenal medulla (AM), and is necessary for adaptation to hypoxia. The mechanisms underlying the detection of changes in O2 tension by these cells are still poorly understood. Recently, we suggested that CB glomus cells have specific metabolic features that favour their sensitivity to hypoxia (Fernandez-Aguera et al, 2015, Cell Metab.).
To investigate the metabolic profile characteristic of acute O2-sensing cells, we used adult mice to compare the transcriptomes of three organs derived from common sympathoadrenal progenitors, but exhibiting variable responsiveness to acute hypoxia: CB and AM which are O2-sensitive (CB > AM) and superior cervical ganglion (SCG), which are practically O2-insensitive. Our data support the concept that responsiveness to acute hypoxia depends on a “signature metabolic profile” in peripheral chemoreceptor cells.

overall_design: The CB, AM, and SCG from 2 months old C57 wildtype mice were used for RNA extraction and hybridization on Affymetrix GeneChip Mouse Transcriptome 1.0 Arrays. Three replicates of CB, and 4 replicates of AM and SCG were included in the current study. Due to the small tissue size, each CB replicate was pooled from 10 mice, whereas each AM and SCG replicate was pooled from 3 mice to obtain enough amount of RNA.

first: Victoria

last: Bonilla-Henao

first: Paula

last: García-Flores

first: Ignacio

last: Arias-Mayenco

first: Patricia

last: Ortega-Sáenz

first: José

last: López-Barneo


title: Diet alters peripheral blood mononuclear cell (PBMC) gene expression profile in dogs; a proof of concept study

city: Lincoln

first: Paul

last: Maclean

address: Cnr Springs Road and Gerald Street

country: New Zealand

institute: AgResearch NZ LTD

summary: Peripheral blood mononuclear cell (PBMC) gene expression profiling is a low-invasive tool used in human diet intervention studies. In dogs this technique has been used to investigate disease states but not to examine the effect of diet. We tested the hypothesis that diet alters dog systemic immune cell gene expression profiles by comparing PBMC gene expression in dogs fed either a premium kibbled diet or a raw red meat diet for 9 weeks. Our results showed that diet shifted the dogs’ PBMC gene expression profile and these alterations corresponded with changes in plasma IgA levels. This illustrates that PBMC microarrays are a useful tool that may be applied to study the long-term effects of diet on health outcomes for the dog.

overall_design: Two colour microarray, loop design. 2 treatments (either kibble diet or meat diet) with 4 timepoints (Start of experiment: timepoint 0 and one measurement every 3 weeks for 9 weeks). All sample types: Canis lupus familiaris PBMC. Biological replicates: 6

first: Wayne

last: Yong

first: Rachel

last: Anderson


title: SIRT1 expression effect on migration and invasion of gastric cancer cells

city: Jinan

first: Guoying

last: Dong

state: Shandong

address: Jinan lixia district Wenhua west road no. 44

department: Cheeloo College of Medicine

institute: Shandong University

summary: Analysis of BGC-823 gastric cancer cells with SIRT1 overexpression or knockdown. SIRT1, a NAD+-dependent protein deacetylase, exerts inhibitory effects on migration and invasion of gastric cancer. Results provide insight into the role of  SIRT1 in the metastasis of gastric cancer.

overall_design: Four groups: Group 1, Stable lentivirus  infected  BGC-823 cells with the lentiviral expressing vector. Group 2, Stable lentivirus infected BGC-823 cells with the lentiviral  expressing vector containing SIRT1 cDNA sequence. Group 3, Stable lentivirus infected BGC-823 cells with the lentiviral vector containing interference control sequence. Group 4, Stable lentivirus infected BGC-823 cells with the lentiviral vector containing interference sequence targeting SIRT1.

first: Qing

last: Yang


title: RNase 7 strongly promotes TLR9-mediated DNA sensing by human plasmacytoid dendritic cells

city: Hannover

first: Verena

last: Kopfnagel

address: Carl-Neuberg-Straße 1

department: Dermatology

country: Germany

institute: Hannover Medical School

summary: We show here that the antimicrobial peptide RNase 7 enables human pDCs to recognize self-DNA, and promotes their rapid sensing of bacterial DNA.

overall_design: The microarray design is based on a dual-color approach comparing mRNA expression in treated versus untreated cells of one donor, giving rise to one dual-color microarray experiment. A second microarray experiment was performed with samples from a second donor including a dye-swap. In order to enable inspection of intensity values, dual-colour results were integrated into a single-color GEO matrix.

first: Thomas

last: Werfel

first: Sylvia

last: Wagenknecht

first: Jürgen

last: Harder

first: Karsten

last: Hofmann

first: Michael

last: Kleine

first: Anna

last: Beate Sodeik


title: Gene expression profiles of breast, colorectal, prostate, and non-small cell lung cancer

city: New York

first: Wei-Yi

last: Cheng

state: New York

address: Roche Translational and Clinical Research Center, 430 East 29th Street

department: Pharma Research and Early Development

institute: Roche Innovation Center New York

summary: Gene expression profiles from 280 formalin-fixed and paraffin embedded normal and tumor samples of four cancer types

overall_design: 65 breast cancer with 10 matched normal; 57 colorectal cancer with 12 matched normal; 60 non-small cell lung cancer with 9 matched normal; 60 prostate cancer with 7 matched normal

first: Jurriaan

last: Brouwer-Visser

last: Bauer-Mehren

first: Daniela

last: Maisel

first: Katharina

last: Lechner

first: Emilia

last: Andersson

first: Joel

middle: T

last: Dudley

first: Francesca

last: Milletti


title: Expression data from sclerosing epithelioid fibrosarcoma (SEF) tumors

city: Lund

first: Elsa

last: Arbajian

address: klinikgatan 28, BMC C13

department: Clinical genetics

country: Sweden

institute: Lund University

type:
Expression profiling by array
Third-party reanalysis

summary: We used microarrays to detail the global programme of gene expression in SEF tumors and to identify up- and down- regulated genes compared to tumors previously deposited in GEO

overall_design: 10 samples of SEF tumors were analyzed, in addition to the tumors previously deposited in GEO.

first: Fredrik

last: Mertens


title: Discovering the process of bladder healing as the milestone for its regeneration

city: Bydgoszcz

first: Marta

last: Rasmus

address: Skłodowskiej-Curie 9

country: Poland

institute: Nicolaus Copernicus Univercity in Torun Ludwik Rydygier Collegium Medicum in Bydgoszcz

summary: Molecular mechanism underlying regeneration process, triggered by stem cells in tissue engineered urinary bladder, is still poorly explained. The study aimed to explore underlining pathways associated with regeneration process in urinary bladder reconstructed with stem cell seeded graft. The study was performed on 110 Wistar rats. Urinary bladders were augmented with bladder acellular matrix (BAM)(n=52) or BAM seeded with adipose derived  stem cells (ADSCs)(n=52). The process of bladder healing was analyzed at 7, 30, 90 and 180 days postoperatively. Gene expression was evaluated using microarrays and analyzed in GeneSpring Software. Gene ontology (GO) and pathway enrichment analyses of differentially expressed genes (DEGs) were performed. A total of 4023, 4674, 7997 and 1120 of DEGs between the bladders augmented with ADSCs seeded BAM and BAM only were identified at 7, 30, 90 and 180 days postoperatively, respectively. The DEGs were enriched in GO terms associated with cellular and intercellular events, morphogenesis, epithelium, smooth muscles and nerves regeneration, angiogenesis, inflammatory response and wound healing. Numerous differentially expressed pathways between the bladders augmented with ADSCs seeded BAM and BAM only were identified. In conclusion, this study provided the unequivocal evidence that stem cells changed healing milieu in tissue engineered urinary bladder and indicated underlying pathways that can be associated with regeneration process triggered by stem cells.

last: Pokrywczynska

first: Karolina

last: Warda

first: Arkadiusz

last: Jundzill

first: Lukasz

last: Buchholz

first: Daria

last: Balcerczyk

first: Jan

last: Adamowicz

first: Tomasz

last: Drewa


title: BRD4 promotes distinct transcriptional programs in bulk and stem-like prostate tumor cells

status: Public on Sep 06 2017

city: Bellinzona

first: Carlo

last: Catapano

address: Via Vela 6

department: Experimental therapeutics

country: Switzerland

institute: IOR

summary: Genetic knockdown or chemical inhibitors of BRD4 elicited different biological responses in bulk tumor cells in 2D cultures and CSC-enriched tumor-sphere cultures. Gene profiling revealed that BRD4 inhibition affected different sets of genes in two cell contexts. BRD4 drives a CSC-specific transcriptional programs that can be disrupted by chemical inhibitors causing exhaustion and elimination of prostate CSCs.

overall_design: Total RNA obtained from prostato-spheres and adherent cells was compared.  Additionally Total RNA obtained from prostato-spheres and adherent cells after OTX015 treatment at 0, 4 and 24 h was measured and compared.

first: Gianluca

last: Civenni

first: Roberto

last: Bosotti

middle: V


title: Half-lives mRNA analysis of Stenotrophomonas maltophilia D457 and rng-deficient mutant

city: Madrid

first: Alejandra

middle: Leticia

last: Bernardini

state: Madrid

address: Darwin 3

institute: Centro Nacional de Biotecnología

summary: We calculated half-life values of mRNAs quantified by RNA-Seq by a suitable method of normalization. We determined the half-lives of more than 2200 mRNAs in the Stenotrophomonas maltophilia D457 wild-type strain and in an isogenic RNase G deficient mutant. Median half-lives were 2,74 and 3 min in the wild-type and the rng-deficient mutant respectively. We found an overall enhancement of half-life times of mRNAs when the gene encoding RNase G is lacking, showing that many RNAs are targets of RNase G in S. maltophilia. For achieving such goal, we propose a method for the normalization of RNA-Seq based studies on global bacterial mRNA decay.

overall_design: A RNA run-out experiment was carry out adding rifampicin to S. maltophilia D457 and rng-interrupted mutant growing at exponential phase. RNA was sequenced by RNASeq Illumina and quantified to calculated RNA half-lives.

middle: L

first: José

last: Martinez


title: Gene expression profiling of experimental-induced pulmonary fibrosis in subcutaneous bleomycin-treated mice vs EXT-treated mice

first: Anna

last: Löfdahl

address: Klinikgatan 30

department: Experimental Medical Science

institute: Lund University, BMC

summary: Analysis of whole genome gene expression levels in distal lung tissue from mice with systemically bleomycin-induced pulmonary fibrosis. The hypothesis is that bleomycin promotes a specific genotype associated with development of pulmonary fibrosis and that treatment with compound EXT reduces the induction of genes related to the early progression of fibrosis.

overall_design:
Total RNA was isolated from distal lung tissue after 2 weeks s.c. treatment with bleomycin, with or without p.o. treament with EXT5 or EXT9. Comparisons of gene expression levels were made with healthy controls vs bleomycin-treated mice, with or without EXT-treatment. 6 mice (biological replicates) per treatment group were analyzed.
Data were presented from two Ilumina microarray analyses with samples 1-7 and 8-14 included in first run. Second run contained samples 22-27 and 36-42, along with samples 3, 5, 7, 12 and 14 (re-analyzed) for the verification of non existing interassay variation. Data were presented as combined data from two seperate arrays.

The arrays and analysis were performed by SCIBLU Genomics facility, Lund University (Lund, Sweden) and NBIS (National Bioinformatics Infrastructure Sweden).

first: A

first: K

last: Rydell-Törmänen

first: A-K

last: Larsson-Callerfelt

first: C

last: Wenglén

first: G

last: Westergren-Thorsson


title: Identification of genes involved in the cell growth arrest by knockout of BAG3 in human cervical carcinoma HeLa cells

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

institute: University of Toyama

summary:
BAG3 (BCL2-associated athanogene 3) is a member of the BAG protein family. BAG3 affects a wide variety of cellular events including cell proliferation, apoptosis and autophagy. Recently our data demonstrated that knockout (KO) of BAG3 induces the cell growth arrest in human cervical carcinoma HeLa cells.
In the present study, to identify genes involved in the cell growth arrest by BAG3-KO in HeLa cells, global-scale gene expression analysis was carried out using a GeneChip® system.

overall_design: Human cervical carcinoma cell line HeLa cells (wild type), and BAG3-KO HeLa cells (clone 1 and clone 2) were used. These cells were cultured in Eagle's Minimum Essential medium supplemented with 10% fetal bovine serum at 37°C. Total RNA samples were prepared from the cells, and quality of the RNA was analyzed using a Bioanalyzer 2100. Gene expression was analyzed by an Affymetrix GeneChip® system with a Human Genome U133-plus 2.0 array. Sample preparation for array hybridization was carried out as described in the manufacturer’s instructions.

first: Tetsushi

last: Hirano

first: Yukihiro

last: Furusawa


title: Human dermal fibroblast reprogramming: compact and differentiated colonies during maturation phase

city: México

first: Karlen

last: Gazarian

state: Mexico

address: Circuito Exterior 3

department: Genomic Medicine

institute: Instituto de Investigaciones Biomédicas

summary: Transcriptional profiling of reprogrammed cells at day 20 post-transduction comparing compact and differentiated colonies with established induced Pluripotent Stem Cells (iPSC) generated from human dermal fibroblasts (HDF). This study focused in the identification of upregulated transcription factors related to early developmental processes, particularly during primitive streak formation.

overall_design: Compact embryonic stem cell-like colonies and differentiated polygonal cell-containing colonies at day 20 after reprogramming vector transduction into HDF, isolated from three different reprogramming experiments; and undifferentiated colonies from and established iPSC line, at passage 20. One replicate for compact and differentiated samples. Two replicates for iPSC sample.

first: Ricardo

middle: R

last: Cevallos

first: Griselda

last: Rodriguez

middle: G


title: Silencing of Retrotransposons by SETDB1 Inhibits the Interferon Response in Acute Myeloid Leukemia: Data for CRISPR Screen, ChIP-seq, RNA-seq, and Stranded RNA-seq in THP-1 Cells

city: Princeton

first: Trinna

middle: L.

last: Cuellar

state: New Jersey

address: Lewis Thomas Lab, Washington Rd/MOF223C

institute: Princeton University

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

overall_design: Refer to individual Series


title: GRO-seq in human CD34+ erythrocytes

city: Cambridge

first: Xiaofei

last: Gao

state: MA

institute: Whitehead Institute for Biomedical Research

summary:
Purpose: GRO-seq is a robust method to examine the nascent RNA transcriptome in the genome level
Methods: The GRO-seq measures the trancription of nascent RNAs in the genome. From human CD34+ erythrocytes treated with veichle or T4 we conducted GRO-seq to examine the transcripome.

overall_design: Analysis of nascent RNA with GRO-seq in human CD34+ derived erythroblasts  treated for 6 hrs with 1 μM GC-1 or with vehicle

first: Harvey

middle: F

last: Lodish


title: Gene expression profiles of hiPSC-derived retinal ganglion cells in MT-ND4 mutated Leber's hereditary optic neuropathy

city: Taipei

first: Aliaksandr

last: Yarmishyn

address: No. 201, Section 2, Shipai Road, Beitou District

country: Taiwan

institute: Taipei Veterans General Hospital

summary: Leber’s hereditary optic neuropathy (LHON) is a maternally inherited mitochondrial disease caused by homoplasmic mutations in complex I subunit genes, and is characterized by incomplete penetrance. The mechanism of low penetrance of complex I mutation is still largely unclear today. In this study, we created the patient-specific induced pluripotent stem cells (iPSCs) from MT-ND4 mutated LHON affected patient, asymptomatic mutation carrier and control, and differentiated them into retinal ganglion cells (RGCs) for pathogenesis survey. We observed the following phenotypic features in the LHON-specific RGCs as compared to the control: 1) enhanced mitochondrial biogenesis in affected and carriers; 2) compensatory increased mitochondrial complex I activity in carrier, but not in affected patient; 3) reduced spare respiratory activity in affected and carrier. Microarray profiling of LHON-specific RGCs revealed abundant overexpression of genes encoding components of cell cycle regulation machinery as compared to the control.

overall_design: Total RNA was isolated from iPSC-derived RGCs of the control (NTA), LHON disease affected (LF3) and unaffected mutation carrier (0707). Thus, three samples were analyzed.

first: Y

last: Wu

first: S

middle: H

last: Chiou


title: Caloric restriction affects small RNA expression in mouse hepatic mitochondria

city: Beijing

first: De-Pei

last: Liu

address: Dong Dan San Tiao 5, Dongcheng District

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

summary: MicroRNAs (miRNAs) are crucial post-transcriptional regulators that extensively affect protein synthesis. Emerging evidence suggests the presence of miRNAs in mitochondria and important regulatory roles of miRNAs in mitochondrial translation. To investigate whether miRNAs are involved in the CR-induced mitochondrial translational changes, we used small RNA sequencing to profile miRNA expression in whole liver tissue as well as in liver mitochondria. The sequencing results revealed that the number of miRNAs identified in mitochondria was comparable to that found in the whole tissue.

overall_design: We used small RNA sequencing to profile miRNA expression in ad libitum vs. calorie-restricted mouse liver tissue and in liver mitochondria.

first: Ran

last: Zhang

first: Hou-Zao

last: Chen

first: Xu

last: Wang

first: Jia-Hua

last: Qu


title: Early- and late-onset preeclampsia and the tissue-specific epigenome of the placenta and newborn

city: Leiden

first: Roderick

last: Slieker

address: PO Box 9600

department: Medical Oncology

institute: Leiden University Medical Center

summary:
Introduction. Preeclampsia (PE) carries increased risks of cardiovascular- and metabolic diseases in mothers and offspring during the life course. While the severe early-onset PE (EOPE) phenotype originates from impaired placentation in early pregnancy, late-onset PE (LOPE) is in particular associated with pre-existing maternal cardiovascular- and metabolic risk factors. We hypothesize that PE is associated with altered epigenetic programming of placental and fetal tissues and that these epigenetic changes might elucidate the increased cardiovascular- and metabolic disease susceptibility in PE offspring.
Methods. A nested case-control study was conducted in The Rotterdam Periconceptional Cohort comprising 13 EOPE, 16 LOPE, and three control groups of 36 uncomplicated pregnancies, 27 normotensive fetal growth restricted (FGR) and 20 normotensive preterm birth (PTB) complicated pregnancies. Placental tissue, newborn umbilical cord blood leucocytes (UC-WBC) and umbilical vein endothelial cells (HUVEC) were collected and DNA methylation of cytosine-guanine dinucleotides was measured by the Illumina HumanMethylation450K BeadChip. An epigenome-wide analysis was performed by using multiple linear regression models.
Results. Epigenome-wide tissue-specific analysis between EOPE and PTB controls revealed 5001 mostly hypermethylated differentially methylated positions (DMPs) in UC-WBC and 869 mostly hypomethylated DMPs in placental tissue, situated in or close to genes associated with cardiovascular-metabolic developmental pathways.
Discussion. This study shows differential methylation in UC-WBC and placental tissue in EOPE as compared to PTB, identifying DMPs that are associated with cardiovascular system pathways. Future studies should examine these loci and pathways in more detail to elucidate the associations between prenatal PE exposure and the cardiovascular disease risk in offspring.

overall_design: Controls: 25 blood, 25 placenta, 25 HUVEC; EOPE: 10 blood, 8 HUVEC, 11 placenta; FGR: 24 blood, 18 HUVEC, 20 placenta; LOPE: 13 blood, 10 HUVEC, 11 placenta; PTB: 16 blood, 14 HUVEC, 15 placenta.

first: Emilie

last: Herzog

first: Alex

middle: J

last: Eggink

first: Sten

last: Willemsen

middle: C

first: Janine

last: Felix

first: Andrew

last: Stubbs

first: Peter

last: van der Spek

first: Joyce

last: Van Meurs

first: Bastiaan

last: Heijmans

first: Régine

last: Steegers-Theunissen


title: Expression data from lung metastatic explants

city: Montreal

first: Julie

last: St-Pierre

state: Quebec

address: 3655 Promenade Sir William Osler

department: Department of Biochemistry

country: Canada

institute: McGill University

summary:
The role of PGC1alpha in breast cancer lung metastasis is largely unknown. We used expression data from lung metastatic explants overexpressing PGC1alpha or control, treated with phenformin to understand global gene expression changes which occur in a PGC1alpha context and under phenformin treatment.
We used expression data to understand the pathways and genes that may lead to lung metastasis in a PGC1alpha overexpression setting.

overall_design: PGC1alpha overexpressing or control explants from a lung metastatic tail vein (LMTV) assay were isolated and put into culture and treated with phenformin (100uM) for 4 days or dh20 control.

first: Sylvia

last: Andrzjewski

first: Radia

last: Johnson

first: Sébastien

last: Tabariès

first: Matthew

last: Annis


title: Genome-wide maps of chromatin state in human erythroblasts differentiated from CD34+ cells.

first: Xiaofei

last: Gao

summary: Treatment with thyroid hormone receptor beta agonist, GC-1, significantly increased the signal intensities of the top 300 NCOA4 chromatin binding sites, which overlapped with binding sites for Pol II as well as with histone marks associated with active transcription, such as H3K27Ac and H3K4Me3, but not with marks such as H3K4Me1 commonly associated with enhancers

overall_design:
Examination of chromatin occupancy of NCOA4, RNA polymeriase, and histone modifications in human CD34+ derived erythroblasts.
------------------------------
Authors indicate that peaks were not called for H3K27Ac_GC1_ChIPSeq, H3K4Me3_GC1_ChIPSeq, NCOA4_untreated_ChIPSeq, H3K4Me1_GC1_ChIPSeq, and PolII_GC1_ChIPSeq.

first: Harvey

last: Lodish


title: NCOA4


title: Expression data from lung metastasis

summary:
The role of PGC1alpha in breast cancer lung metastasis is largely unknown. We used expression data from lung metastasis of mice injected with PGC1alpha overexpression or control cells to understand global changes that occur upon overexpression of PGC1alpha that lead to lung metastasis.
We used expression data to understand the pathways and genes that may lead to lung metastasis in a PGC1alpha overexpression setting.

overall_design: Mice were injected by tail vein with either PGC1alpha overexpressing or control  cells (NMuMG-ErbB2/PGC-1alpha and NMuMG-ErbB2/VC cells ) respectively. Mice were treated with phenformin for 1 week or PBS control. Lung metastasis was isolated by laser capture microdissection.


title: Identification of genes involved in basal cell carcinoma of the eyelid

status: Public on Sep 05 2017

first: Yoshiaki

last: Tabuchi

summary:
Basal cell carcinoma (BCC) is the most frequent malignant tumor of the eyelid. However, there is limited understanding of how altered gene expression of BCC of the eyelid related to the pathogenesis.
In this study, to identify genes involved in basal cell carcinoma of the eyelid, global-scale gene expression analysis was carried out using a GeneChip® system.

overall_design: Total RNA was extracted from BCC of the eyelid and normal human epidermal keratinocytes (NHEK). Quality of the RNA was analyzed using a Bioanalyzer 2100. Gene expression was analyzed by an Affymetrix GeneChip® system with a Human Genome U133-plus 2.0 array. Sample preparation for array hybridization was carried out as described in the manufacturer’s instructions.

first: Tatsuya

last: Yunoki


title: Expression data from a human lung metastatic cell line treated with siPGC1alpha or siControl

summary:
To understand global expression changes in a knockdown of PGC1alpha (siPGC1alpha) vs control (siControl) in a lung metastatic cell line (4175)
Metabolic adaptations play a key role in fuelling tumour growth. However, less is known regarding the metabolic changes that promote cancer progression to metastatic disease. Herein, we reveal that PGC-1a expression and activity are differentially regulated depending on breast cancer metastatic sites. Breast cancer cells that preferentially metastasize to lung display striking upregulation of PGC-1a expression. PGC-1a promotes breast cancer cell migration and invasion in vitro and augments lung metastasis in vivo. MDA-MB-231 lung variant (4175) cells were treated with a short interfering RNA (siRNA) for human PGC-1a (PPARG1A) or control siRNA for 48hrs 24 hours post-plating cells.


title: Human microRNA (miRNA) expression during serum starvation

city: New Delhi

first: Sandeep

last: Saxena

state: New Delhi

address: Aruna Asaf Ali Marg

country: India

institute: National Institute of Immunology

summary: The study aimed to identify the differentially regulated microRNAs during serum starvation. We identified miRNAs exhibiting altered expression in asynchronous, serum starved and serum re-supplemented human cells. We identified several miRNAs that were upregulated following serum starvation and downregulated upon serum re-supplementation.

platform_organism:
Homo sapiens
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Macacine alphaherpesvirus 1
Human betaherpesvirus 5
human gammaherpesvirus 4
Herpesvirus saimiri (strain 11)
JC polyomavirus
Human immunodeficiency virus 1
Human betaherpesvirus 6B
Human gammaherpesvirus 8
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: Human cells were grown in serum free media for 48 h, after which cells were re-supplemented with fresh media containing 10% fetal bovine serum and further grown for 12 h. Asynchronously growing cells were used as control. Three-condition experiment: Asynchronous (control) vs. Serum starved vs. Serum Re-supplemented. Biological replicates: 2.

first: Tanushree

last: Ghosh

first: Akhil

last: Varshney


title: Transcriptional reference map of hormone responses in wheat spikes

city: Wenjiang, Chengdu city

first: Yunfeng

last: Jiang

state: Sichuan

address: Huiming road No.211

institute: Triticeae Research Institute, Sichuan Agricultural University

summary:
Phytohormones are key regulators of plant growth, development, and signalling networks involved in responses to diverse biotic and abiotic stresses. Transcriptional reference maps of hormone responses have been reported for several model plant species such as Arabidopsis thaliana, Oryza sativa, and Brachypodium distachyon. However, because of species differences and the complexity of the wheat genome, these transcriptome data are not appropriate reference material for wheat studies.
We comprehensively analysed the transcriptomic responses in wheat spikes to seven phytohormones, including indole acetic acid (IAA), gibberellic acid (GA), abscisic acid (ABA), ethylene (ET), cytokinin (CK), salicylic acid (SA), and methyl jasmonic acid (MeJA). A total of 3386 genes were differentially expressed at 24 h after the hormone treatments. Furthermore, 22.7% of these genes exhibited overlapping transcriptional responses for at least two hormones, implying there is crosstalk among phytohormones. We subsequently identified genes with expression levels that were significantly and differentially induced by a specific phytohormone (i.e., hormone-specific responses). The data for these hormone-responsive genes were then compared with the transcriptome data for wheat spikes exposed to biotic (Fusarium head blight) and abiotic (water deficit) stresses.
Our data were used to develop a transcriptional reference map of hormone responses in wheat spikes.

overall_design: Only flowering heads were used for hormone treatments. Two florets of each fully developed spikelet from a whole spike at the mid-anthesis stage were treated with 10 μl 10% methanol:water solution with or without (control) 2 mM IAA, 1 mM SA, 1 mM MeJA, 0.38 mM ABA, 0.5 mM GA3, or 0.5 mM trans-zeatin (a type of cytokinin). Regarding the ET treatment, each head was sealed in a plastic bag with 2 ml freshly prepared 25 mM ethephon (pH = 11). All of the hormone solutions were used to treat florets within 1 h of being prepared. The heads were collected at 24 h after the hormone treatments, and then ground to a fine powder in liquid nitrogen. Each treatment was completed with three biological replicates, each of which comprised at least five heads. No unusual morphological changes were observed in the treated heads. The hormone concentrations of the treatments were based on previous studies

first: Peng-Fei

last: Qi

first: Yun-Feng

first: You-Liang

last: Zheng


title: Control of brain tumor growth by reactivating monocytes and macrophages with niacin

city: Calgary

first: Voon

middle: Wee

last: Yong

state: Alberta

address: 3330 Hospital drive NW

department: Clinical Neurosciences

institute: University of Calgary

summary: We have found that innate immune cells (monocytes/macrophages) are compromised in malignant glioma, and we have determined that vitamin B3 (niacin) reactivates and/or reprograms monocytes/macrophages to inhibit glioma growth, particularly by suppressing the growth of brain tumor initiating cells (BTICs).  To this end, we sought to obtain insights into the mechanisms by which niacin regulates monocyte/macrophage activity to alter glioma growth.  Analysis of the microarray data identified several genes that were differentially altered in niacin-treated monocytes that could regulate BTIC growth.  The study has identified a mechanistic basis for the regulation of glioma growth with niacin treatment.

overall_design: Monocytes were isolated from the blood of three normal adult individuals.  Each set of monocytes was treated with niacin (100 μM) for 6h in serum free BTIC medium, or were left untreated as control.  After 6h, RNA was extracted using RNeasy MiniKit (Qiagen) as per manufacturer’s instruction, and subjected to microarray analysis.  Thus, there were 3 separate sets of monocytes, each with control or niacin groups.

first: V

middle: W

first: Susobhan

last: Sarkar

first: Reza

last: Mirzaei


first: Trinna

last: Cuellar

summary: We performed H3K9me3 chIP-seq 5 days following disruption of the SETDB1 H3K9 trimethylase with two different sgRNAs (6, and 9) or non-targeting control. Our data suggests that H3K9me3 is modestly reduced over transposable elements and some ZNF genes following disruption of SETDB1.

overall_design: Examination of H3K9me3 levels over standard genes and transposable elements in THP-1 cells following disruption of SETDB1

first: Xioatian

last: Zhang


title: Stem cell-like properties of CK2β-downregulated mammary cells [mRNA]

city: GRENOBLE

first: Odile

last: FILHOL

address: 17, rue des martyrs

department: BIG

country: France

institute: INSERM-CEA

summary: The ubiquitous Protein kinase CK2 has been demonstrated to be overexpressed in a number of human tumors. This enzyme is composed of two catalytic α or α’ subunits and a dimer of β regulatory subunits whose expression levels are probably implicated in CK2 regulation. Several recent papers reported that unbalanced expression of CK2 subunits is sufficient to drive epithelial to mesenchymal transition, a process involved in cancer invasion and metastasis. Herein, through transcriptomic and miRNA analysis together with comparison of cellular properties between wild type and CK2β-knock-down MCF10A cells, we show that down-regulation of CK2β subunit in mammary epithelial cells induces the acquisition of stem cell-like properties associated with CD44high/CD24low antigenic phenotype and the ability to grow under anchorage-independent conditions. These data demonstrate that a CK2β level establishes a critical cell fate threshold in the control of epithelial cell plasticity. Thus, this regulatory subunit functions as a nodal protein to maintain an epithelial phenotype.

overall_design: The microarray analysis was performed with RNAs isolated from Mock and ΔCK2β-derived MCF10A cells, each from two independent cell cultures (duplicates).

first: E

last: Duchemin-Pelletier

last: Spreux

first: M

last: Baulard

last: Prioux

last: Burute

last: Mograbi

first: L

last: Guyon

last: Théry

first: C

last: Cochet

first: O

last: Filhol


title: Stem cell-like properties of CK2β-downregulated mammary cells [miRNA]

overall_design: The microarray analysis was performed with RNAs isolated from mock and ΔCK2β-derived MCF10A cells, each from two independent cell cultures (duplicates).


title: RNA sequencing to determine the contribution of kinase receptor transactivation to G protein coupled receptor signalling in vascular smooth muscle cells

city: Bundoora

first: Nitin

last: Mantri

state: Victoria

address: Plenty Road

department: School of Science

country: Australia

institute: RMIT University

summary: G protein coupled receptor (GPCR) signalling covers three major mechanisms. GPCR agonist engagement allows for the G proteins to bind to the receptor leading to a classical downstream signalling cascade. The second mechanism is via the utilization of the β-arrestin signalling molecule and thirdly via transactivation dependent signalling. GPCRs can transactivate protein tyrosine kinase receptors (PTKR) to activate respective downstream signalling intermediates. In the past decade GPCR transactivation dependent signalling was expanded to show transactivation of serine/threonine kinase receptors (S/TKR). Kinase receptor transactivation enormously broadens the GPCR signalling paradigm. This work utilizes next generation RNA-sequencing to study the contribution of transactivation dependent signalling to total protease activated receptor (PAR)-1 signalling. Transactivation, assessed as gene expression, accounted for 50 percent of the total genes regulated by thrombin acting through PAR-1 in human coronary artery smooth muscle cells. GPCR transactivation of PTKRs is approximately equally important as the transactivation of the S/TKR with 209 and 177 genes regulated respectively, via either signalling pathway. This work shows that genome wide studies can provide powerful insights into GPCR mediated signalling pathways

overall_design: Human CASMCS cells were subject to various treatments: basal, thrombin, thrombin + SB, thrombin + AG and thrombin + SB + AG. Gene expression was studies after 30 minutes to assess genes that are differentially expressed by treat emnt with agonists and antagonists. The agonoists and antagonists are associated with transactivation of GPCRs and the gene expression results will help identify relevant genes.

first: Danielle

last: Kamato

first: Vijay

last: Bhaskarla

first: Peter

last: Little

first: Narin

last: Osman


title: Stem cell-like properties of CK2β-downregulated mammary cells


title: Heterogeneity of p53 dependent genomic responses following ethanol exposure in a developmental mouse model of fetal alcohol spectrum disorder

city: Syracuse

first: Frank

middle: A

last: Middleton

state: NY

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

summary: This study examined if p53 was essential in the brain’s response to alcohol using a mouse model of fetal alcohol spectrum disorder (FASD) that involved the equivalent of a single day of binge drinking. We quantified the amount of cell death in specific brain regions and examined the levels of gene expression in these regions 8 hours after alcohol exposure using RNA-seq. Contrary to expectations, we found that cell death still occurred at the same or greater level in the brains of mice lacking p53 as in normal mice. However, we also found evidence that the lack of p53 greatly affected the expression of groups of genes involved in brain cell communication and metabolism.

overall_design: Somatosensory cortex was removed from wildtype (WT) and p53 knockout (KO) male mice on postnatal day 7, 8 hours after an IP injection of ethanol. Brains were flash frozen on dry ice, and RNA was harvested using Trizol reagent followed by RNeasy (Qiagen). Illumina Stranded RNA libraries were prepared using the RS-122-2101 Sample Prep Kit with 200-300 nanograms of total RNA for the starting material.


title: Far Infrared Radiation Promotes Renal Proximal Tubule Cell Proliferation Functional Characteristics and Has Protective Effects against Cisplatin Nephrotoxicity

first: Tai

middle: Horng

last: Young

address: No.1 Jen Ai Rord Section 1

institute: College of Medicine and College of Engineering, National Taiwan University

summary: Far infrared radiation (FIR), a subdivision of the electromagnetic spectrum, has been proved to be beneficial for long-term effects of tissue healing, anti-inflammation, promoting growth, modulating sleep, acceleration of microcirculation, and pain relief. We attempt to study whether FIR would be beneficial for renal proximal tubule cell (RPTC) cultivation and renal tissue engineering. We observed the FIR effects on RPTCs, including cell viability, functional characteristics, immunofluorescence presentations, and subcellular findings. And the FIR protective effects would be further examined with HK-2 cell (Human proximal tubule cell line) against cisplatin, a nephrotoxic agent.  Our study showed that daily exposure to FIR for 30 minutes could significantly increase rabbit RPTC viability in vitro assessed by MTT assay. FIR is not only beneficial in RPTC cell viability. RPTCs with FIR exposure presented higher expression of Na-K ATPase and GLUT1 (Glucose Transporter 1). The finding was documented with western blot analysis with statistical significance. With Q-PCR, CDK5R1, GNAS, NPPB, and TEK expressions were significantly enhanced. With HK-2 cell, the proximal tubule cell line, FIR had protective effects against cisplatin nephrotoxicity through reducing apoptosis.  FIR is a potential photomodulation therapy to facilitate RPTC cultivation with higher cell viability and better functional chanacteristics and would possibly be applied in further nephrotoxicity protection and other cisplatin-sensitive cell protection.

overall_design: Two samples are analyzed, one is human renal proximal tubule cell under FIR treatment, the other is human renal proximal tubule cell under normal condition. The control sample is human renal proximal tubule cell under normal condition.

first: I

middle: N

last: Chiang

first: Yeong

middle: S

last: Pu

first: Chao

middle: Y

last: Huang


title: Increased adaptative immune response and proper feedback reguation protect against clinical Dengue

city: Paris

first: Anavaj

last: Sakuntabhai

address: 28 rue du Dr Roux

department: Genome and Genetics

institute: Institut Pasteur

summary: Clinical symptoms of dengue virus (DENV) infection, the most prevalent arthropod-borne viral disease, range from classical mild dengue fever to severe, life-threatening dengue shock syndrome. However, most DENV infections cause few or no symptoms. Asymptomatic DENV-infected patients provide a unique opportunity to decipher the host immune responses leading to virus elimination without negative impact on an individual’s health. We used an integrated approach of transcriptional profiling and immunological analysis to compare a Cambodian population of strictly asymptomatic viremic individuals with clinical dengue patients. Whereas inflammatory pathways and innate immune response pathways were similar between asymptomatic individuals and clinical dengue patients, expression of proteins related to antigen presentation and subsequent T and B cell activation pathways were differentially regulated, independent of viral load and previous DENV infection history. Feedback mechanisms controlled the immune response in asymptomatic viremic individuals, as demonstrated by increased activation of T cell apoptosis-related pathways and FcγRIIB signaling associated with decreased anti-DENV specific antibody concentrations. Taken together, our data illustrate that symptom-free DENV infection in children is associated with determined by increased activation of the adaptive immune compartment and proper control mechanisms, leading to elimination of viral infection without excessive immune activation, with implications for novel vaccine development strategies

overall_design: 33 Dengue patients samples analyzed, no replicates

first: Etienne

last: Simon-Lorière

first: Veasna

last: Duong

first: Ahmed

last: Tawfik

first: Sivlin

last: Ung

first: Sowath

last: Ly

first: Isabelle

last: Casadémont

first: Matthieu

last: Prot

first: Noémie

last: Courtejoie

first: Kevin

last: Bleakley

first: Philippe

last: Buchy

first: Arnaud

last: Tarantola

last: Dussart

first: Tineke

last: Cantaert


title: Expression data from a lung metastatic cell line or metastatic explants in mouse and human

first: Julie

last: St-Pierre

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Polycomb-like proteins link the PRC2 complex to CpG islands

city: Marburg

first: Robert

last: Liefke

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute of Molecular Biology and Tumor Research (IMT)

institute: Philipps University of Marburg

summary: The Polycomb repressive complex 2 (PRC2) mainly mediates transcriptional repression and has essential roles in various biological processes including the maintenance of cell identity and proper differentiation. Polycomb-like (PCL) proteins, such as PHF1, MTF2 and PHF19, are PRC2-associated factors that form sub-complexes with PRC2 core components, and have been proposed to modulate the enzymatic activity of PRC2 or the recruitment of PRC2 to specific genomic loci. Mammalian PRC2-binding sites are enriched in CG content, which correlates with CpG islands that display a low level of DNA methylation. However, the mechanism of PRC2 recruitment to CpG islands is not fully understood. Here we solve the crystal structures of the N-terminal domains of PHF1 and MTF2 with bound CpG-containing DNAs in the presence of H3K36me3-containing histone peptides. We show that the extended homologous regions of both proteins fold into a winged-helix structure, which specifically binds to the unmethylated CpG motif but in a completely different manner from the canonical winged-helix DNA recognition motif. We also show that the PCL extended homologous domains are required for efficient recruitment of PRC2 to CpG island-containing promoters in mouse embryonic stem cells. Our research provides the first, to our knowledge, direct evidence to demonstrate that PCL proteins are crucial for PRC2 recruitment to CpG islands, and further clarifies the roles of these proteins in transcriptional regulation in vivo.

overall_design: MTF2, SUZ12 and H3K27me3 ChIP-Seq in mouse ES cells, in Control, MTF2 KO, MTF2 wildtype rescue, MTF2 K339A rescue cells. RNA-Seq was performed in Control and MTF2 knockout cells. Experiments were performed in three biological replicates.

first: Haojie

last: Li

first: Junyi

last: Jiang

first: Jesse

middle: V

last: Kurland

first: Wei

last: Tian

first: Pujuan

last: Deng

first: Weidi

last: Zhang

first: Qian

last: He

first: Dinshaw

last: Patel

first: Martha

last: Bulyk

first: Yang

last: Shi

first: Zhanxin

last: Wang


title: Whole transcriptome sequencing of mouse notochord-derived cells at developmental stages E12.5 and P0

city: Philadelphia

first: Lachlan

middle: James

last: Smith

state: Pennsylvania

address: 371 Stemmler Hall, 3450 Hamilton Walk

department: Department of Orthopaedic Surgery

institute: University of Pennsylvania

summary: Recapitulation of developmental signals represents a promising strategy for treating intervertebral disc degeneration. During development, embryonic notochord-derived cells (NDCs) are the direct progenitors of cells that populate the adult nucleus pulposus (NP) and are an important source of secreted signaling molecules. The objective of this study was to define global gene expression profiles of NDCs at key stages of embryonic disc formation. NDCs were isolated from Shh-cre;ROSA:YFP mice at embryonic day 12.5 and postnatal day 0, representing opposite ends of the notochord to NP transformation. Differences in global mRNA abundance across this developmental window were established using RNA-Seq. Principal component analysis revealed clustering of gene expression at each developmental stage with more than 5000 genes significantly differentially expressed between E12.5 and P0. This study represents the first transcriptome-wide analysis of embryonic NDCs. Results suggest signaling and biosynthesis of NDCs change dramatically as a function of developmental stage.

overall_design: For these studies, we used the Shh-cre;ROSA:YFP mouse model, previously established and shown to express YFP in SHH-expressing notochord cells and their progeny at any developmental stage. Animals were euthanized at two developmental stages, embryonic day 12.5 (E12.5) and postnatal day 0 (P0), representing opposite ends of the notochord to NP transformation. Biological replicates (n=4 at both time points) each consisted of pooled embryos or pups (~6) from a single litter.

first: Sun

last: Peck

first: Kendra

middle: K

last: McKee

first: John

last: Tobias

first: Neil

last: Malhotra

first: Brian

middle: D

last: Harfe


title: Expression data of wildtype and miR-146a-deficient 2D2 transgenic T cells

city: Los Angeles

first: Lili

last: Yang

state: CA

address: 610 Charles E. Young Dr. East, TLSB 3032

department: MIMG

institute: University of California, Los Angeles

summary: We used the Affymetrix GeneChip Mouse Genome 430 2.0 Arrays to compare the gene expression profiles of wildtype and miR-146a-deficient 2D2 transgenic T cells.

overall_design: Naïve CD4 T cells sorted from wildtype and miR-146a-deficient 2D2 Tg mice (denoted as 2D2 and 2D2KO T cells, respectively) were cultured in a 24-well plate at 1x10^6 cells per well for 3 days, in the presence of plate-bound anti-CD3 (5 μg/ml) and anti-CD28 (1 μg/ml). On day 3, cells were collected and total RNAs were isolated for whole-genome gene expression profile analysis using the GeneChip Mouse Genome 430 2.0 Arrays, following a standard Affymetrix microarray protocol (UCLA Clinical Microarray Core).


title: Novel contribution of acetylated histone variant H2A.Z in activation of neo-enhancers in prostate cancer [ChIP-seq]

city: Darlinghurst

first: Fatima

last: Valdes Mora

state: NSW

address: 384 Victoria Street

department: Genomics and Epigenetics

institute: Garvan Institute of Medical Research

summary: Acetylation of the histone variant H2A.Z (H2A.Zac) occurs at active promoters and is associated with oncogene activation in prostate cancer, but its role in enhancer function is still poorly understood. Here we show that H2A.Zac containing nucleosomes are commonly redistributed to neo-enhancers in cancer resulting in a concomitant gain of chromatin accessibility and ectopic gene expression. Notably incorporation of acetylated H2A.Z nucleosomes is a pre-requisite for activation of Androgen receptor (AR) associated enhancers. H2A.Zac nucleosome occupancy is rapidly remodelled to flank the AR sites to initiate the formation of nucleosome-free regions and the production of AR-enhancer RNAs upon androgen treatment. Remarkably higher levels of global H2A.Zac correlate with poorer prognosis. Together these data demonstrate the novel contribution of H2A.Zac in activation of newly formed enhancers in prostate cancer.

overall_design: Genome-wide binding analyses of H2A.Z and H2A.Zac in PrEC, LNCaP full media and LNCaP with or without DHT (5alpha-dihydrotestosterone) stimulation (0, 2h, 4h, 16h) using ChIP-Seq, as well as ChIP-seq for 6 histone marks to partition the genome in LNCaP/PrEC cells into different states.

last: Valdes-Mora

first: Cathryn

middle: M

last: Gould

first: Yolanda

last: Colino-Sanguino

first: Fabian

last: Buske

first: Aaron

middle: L

last: Statham

first: Shalima

last: Nair

first: Susan

last: Clark


title: Molecular Integration of Incretin and Glucocorticoid Action Reverses Immunometabolic Dysfunction and Obesity

status: Public on Sep 04 2017

city: Garching

first: Carmelo

last: Quarta

address: Parkring 13

department: Institute for Diabetes and Obesity

institute: Helmholtz Zentrum München

summary: Chronic inflammation has been proposed to contribute to the pathogenesis of diet-induced obesity. However, scarce therapeutic options are available to treat obesity and the associated immunometabolic complications. Glucocorticoids are routinely employed for the management of inflammatory diseases, but their pleiotropic nature leads to detrimental metabolic side effects. We developed a glucagon-like peptide-1 (GLP-1)-Dexamethasone co-agonist in which GLP-1 selectively delivers Dexamethasone to GLP-1 receptor-expressing cells. GLP-1-Dexamethasone lowers body weight up to 25% in obese mice by targeting the hypothalamic control of feeding and by increasing energy expenditure. This strategy reverses hypothalamic and systemic inflammation while improving glucose tolerance and insulin sensitivity. The selective preference for GLP-1 receptors bypasses deleterious effects of Dexamethasone on glucose handling, bone integrity, and hypothalamus-pituitary-adrenal axis activity. Thus, GLP-1-directed glucocorticoid pharmacology represents an efficacious therapy option for diet-induced immunometabolic derangements and the resulting obesity.

overall_design: To elucidate the in vivo signaling properties of GLP-1/Dexa, we performed unbiased transcriptional profiling (mRNA-seq) of hypothalami from DIO mice treated for 5 days with vehicle, GLP-1/Dexa, Dexamethasone (Dexa) or with GLP-1 at the equimolar doses of 100 nmol/kg. A group of calorie restricted mice with body weight matched to that of GLP-1/Dexa-treated mice was included in order to dissect whether the molecular signatures governed by the conjugate are independent from the induced weight loss. N=5 hypothalamic samples per experimental group were used.

first: Matthias

last: Tschöp


title: Novel contribution of acetylated histone variant H2A.Z in activation of neo-enhancers in prostate cancer

type: Methylation profiling by high throughput sequencing


title: Chromatin proteomics reveals novel combinatorial histone modification signatures that mark distinct subpopulations of macrophage enhancers [ChIP-seq]

city: Berlin

first: Tommaso

last: Mari

address: Robert-Rössle-Str. 10

institute: Max-Delbrück-Centrum für Molekulare Medizin

summary: The activity of enhancers and promoters fine-tunes the transcriptional program of mammalian cells through the recruitment and interplay between cell type-specific and ubiquitous transcription factors. Despite their key role in modulating transcription, the identification of enhancers is challenged by their limited sequence conservation and highly variable distance from target genes. Although enhancers are characterised by the strong enrichment of mono-methylation at lysine 4 of histone H3, mirrored by low tri-methylation at the same residue, a comprehensive list of enhancers-associated histone post-translational modifications (PTMs) is still lacking. We undertook a proteomics investigation, based on chromatin immunoprecipitation combined with mass spectrometry (MS), to identify histone marks specifically associated to cis-regulatory elements in macrophages, focusing on enhancers. We also profiled their plasticity during the transcriptional activation induced by an inflammatory stimulus. The proteomic analysis suggested novel PTM associations, which were validated by analysis of ChIP- and RNA-seq data, whose intersection revealed the existence of novel sub-populations of enhancers marked by specific signatures: the dual mark H3K4me1/K36me2 labels transcription at enhancers, whereas H3K4me1/K36me3 and H3K4me1/K79me2 tag distinct intronic enhancers. While demonstrating that analyzing restricted genomic regions can disclose the combinatorial language of histone modifications, this study highlights the potential of MS-based proteomics in addressing fundamental questions in epigenetics.

overall_design: Chromatin immunoprecipitations of H3 lysine 4 tri- or mono-methylated, H3 lysine 27 acetylated or tri-methylated, H3 lysine 36 di- or tri-methylated or H3 lysine 79 di-methilated followed by multiparallel sequencing performed in RAW264.7 macrophage-like cell line. Experiments were carried out in cells either untreated or treated for 1h or 4 hrs with lipopolysaccharide (LPS). When indicated (FL), cells were also pre-treated for 1h with flavopiridol.

first: Monica

last: Soldi

first: Luciano

last: Nicosia

first: Daniele

last: Musiani

first: Gianluca

last: Sigismondo

first: Alessandro

last: Cuomo

first: Giulio

last: Pavesi

first: Tiziana

last: Bonaldi


title: Tissue and circulating microRNA co-expression analysis reveals potential involvement of miRNAs in the pathobiology of frontal fibrosing alopecia [skin]

city: London

first: John

middle: Alexander

last: McGrath

address: Great Maze Pond

department: St John's Institute of Dermatology

country: United Kingdom

institute: King's College London

summary: Frontal fibrosing alopecia (FFA), a clinical variant of follicular lichen planus, is a predominantly postmenopausal, immune-mediated, inflammatory, primary lymphocytic cicatricial alopecia. FFA mainly involves the scalp, facial hair and eyebrows but also affects other body regions. MicroRNAs (miRNAs) have emerged as potential candidates of pathobiologic, diagnostic and therapeutic interest in chronic inflammatory, fibrotic and autoimmune diseases. To explore miRNAs in FFA for their disease relevance we isolated plasma from venous blood from 10 biopsy-proven treatment-naïve FFA cases and 10 matched controls and undertook miRNA expression analysis using the Human Fibrosis miRNA PCR Array (Qiagen). A separate cohort of 7 active FFA cases and 7 matched healthy controls were ascertained for tissue microRNA analysis and all 14 scalp-biopsy-extracted microRNA samples were subjected to microarray analysis on Affymetrix GeneChip miRNA 4.0 arrays. We generated a list of communities for the two skin tissue networks (cases and controls) and identified cluster centres (exemplars) as representative miRNAs of each community. Twenty exemplars in the control network were significantly enriched in the plasma (control) dataset compared to 27 for FFA. Amongst these, there were 17 miRNAs common in both networks, 9 of which were representative in the FFA disease phenotype. Random Forest analysis suggested that 4 circulating miRNAs (hsa-let-7d-5p, hsa-miR-18a-5p, has-miR-20a-5p and hsa-miR-19a-3p) can discriminate between FFA and controls. Our study of skin and plasma miRNA co-expression highlights circulating miRNAs of potential predictive value as biomarkers that should now be validated in larger cohorts.

overall_design: Expression profiling of miRNA from skin of FFA patients and healthy controls on Affymetrix GeneChip miRNA 4.0 arrays

first: Christos

last: Tziotzios

first: Chrysanthi

last: Ainali

last: Holmes

first: Fiona

last: Cunningham

first: Su

last: Lwin

first: Ioulios

last: Palamaras

first: Kapil

last: Bhargava

first: Janice

last: Rymer

first: Catherine

last: Stefanato

first: Niall

last: Kirkpatrick

first: Sergio

last: Vano-Galvan

last: Petridis

first: David

last: Fenton

first: Michael

last: Simpson

first: Alexandros

last: Onoufriadis


title: Tissue and circulating microRNA co-expression analysis reveals potential involvement of miRNAs in the pathobiology of frontal fibrosing alopecia

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

platform_organism:
Homo sapiens
synthetic construct


title: NLR Nod1 signaling promotes survival of BCR-engaged mature B cells through upregulated Nod1 as a positive outcome

status: Public on Sep 03 2017

first: Kyoko

last: Hayakawa

state: PA

address: 333 Cottman Avenue

country: USA

institute: Fox Chase Cancer Center

summary: BCR ligand-engaged B cells upregulate Nod1 during development. Most mature B cells have up-regulated Nod1 and are sensitive to Nod1 signaling, which increases survival upon exposure to microbial products, as a positive outcome of BCR-engaged mature B cells.

overall_design: Dye-swap pair  for each sample were done on 2 individual arrays.

first: Anthony

last: Formica

first: Yan

last: Zhou

first: Daiju

last: Ichikawa

first: Masanao

last: Asano

first: Yue-Sheng

last: Li

first: Susan

last: Shinton

first: Joni

last: Brill-Dashoff

first: Gabriel

last: Núñez

first: Richard

middle: R

last: Hardy


title: Chromatin proteomics reveals novel combinatorial histone modification signatures that mark distinct subpopulations of macrophage enhancers

first: Tommaso

last: Mari


title: Gene expression profiling in knee cartilage in a rat model of osteoarthritis

status: Public on Sep 02 2017

city: Krakow

first: Marcin

last: Piechota

address: Smetna 12

department: Molecular Neuropharmacology

institute: Institute of Pharmacology PAS

summary: Osteoarthritis (OA) is a chronic degenerative disease that leads to joint failure with pain and disability. Gene regulations are implicated in driving an imbalance between the expression of catabolic and anabolic factors, leading eventually to osteoarthritic cartilage degeneration. The different stages of disease progression are described by the complex pattern of transcriptional regulations. The dynamics in pattern alterations were monitored in each individual animal during the time-course of OA progression.

overall_design: Knee cartilage samples were collected from individual male Wistar rats with monosodium iodoacetate (MIA) induced OA (0, 2, 14, 28 days after the treatment). MIA-treated (3 mg) animals were compared to intact controls. Four replicate samples were analyzed per each experimental group. We used whole-genome microarrays (Affymetrix Rat Gene 2.0 ST) to identify OA-related molecular signatures in the knee cartilage.

first: Katarzyna

last: Starowicz

first: Michal

last: Korostynski


title: Modulation of mitochondrial DNA copy number to induce hepatocytic differentiation of human Amniotic Epithelial cells

city: Clayton

first: Vijesh

last: Vaghjiani

address: 27-31 Wright Street

institute: Hudson Institute of Medical Reaserch

summary: Human amniotic epithelial cells were differentiated into hepatocyte-like cellsfor 28 days and gene expression evaluated. Human amniotic epiethelial cells were encapsulated in barium alginate microcapsules and differentiated into hepatocyte-like cells to create 3D environment for differentiation and gene expression evaluated. The aim of the study was to evaluate changes in gene expression during hepatic diffrentiation and effects of encapsulation on differentiation.

overall_design: Four human epithelial cells samples were used as controls (HAEC 1-4) and same cells were also differentiated into hepatocyte-like cells (HLC 1-4) and encapsulated followed by differentiation (Enc. HLC 1-4)

first: Justin

last: St John


title: Integration of biochemical, biophysical and transcriptomics data for investigating the structural and nanomechanical properties of the yeast cell wall

city: Toulouse

first: Marion

last: Schiavone

address: 135 avenue de Rangueil

department: LISBP

institute: INSA-Toulouse

summary:
Identify the molecular cues (genes) which shape the biochemical composition and the nanomechanical properties of the cell wall of Saccharomyces cerevisae and the links between these two parameters represent a major issue in the understanding of the biogenesis and the molecular assembly of this essential cellular structure, which may have consequences in diverse biotechnological applications.
Firstly, we compared the biochemical and biophysical properties of 4 industrial strains with the laboratory sequenced strain BY4743 and used transcriptome data of these strains to infer biological hypothesis about differences of these properties between strains.
The second approach was to employ a multivariate statistical analysis to identify highly correlated variables among biochemical, biophysical and genes expression data.

overall_design:
Four diploid Saccharomyces cerevisiae strains (named as L69, L71, L62 and L60) were studied and compared to the Saccharomyces cerevsiaie strain BY4743 (from Euroscarf collection).
Three independent biological cultures of each strain were carried out in YPD medium. Total RNA was extracted from these cultures. A total of 15 samples (5 strains made in triplicates) were spotted on Agilent slides.

first: Sébastien

last: Déjean

first: Mathieu

last: Castex

first: Nathalie

last: Sieczkowski

first: Etienne

last: Dague

first: Jean

last: François


title: MiR-1287-5p has inhibitory effects on breast cancer growth mediated by interaction with phosphoinositide 3-kinase CB (miR-1287-5p overexpression study)

city: Graz

first: Martin

last: Pichler

address: Auenbruggerplatz 15

department: Internal medicine, Division of Oncology

country: Austria

institute: Medical University of Graz

summary: Background: Non-coding RNAs and especially microRNAs have been discovered as master regulators of cancer initiation and progression. The aim of our study was to discover and characterize the function of yet uncharacterized microRNAs in human breast carcinogenesis.   Methods:   In an unbiased approach, we made use of a commonly used model system for breast cancer (BC) stem cells (“mammospheres”) to identify whole miRNome alterations with a special focus on previously uncharacterized miRNAs in BC. We further characterized the influence of microRNA-1287-5p, a yet uncharacterized microRNA in BC, in patient samples (n=1262) and on several hallmarks of cancer in vitro and in vivo with a special focus on triple negative BC. The molecular mode of action was further characterized using whole transcriptome analysis, in silico prediction tools, miRNA-interaction luciferase assays and pheno-copy assays.   Results:   We identified miR-1287-5p among many others as differentially expressed in mammospheres. Clinical validation indicated that miR-1287-5p is significantly downregulated in human BC and associated with poor prognosis. This clinical finding can be explained by miR-1287-5p mediated growth inhibitory effects, G1 cell cycle arrest, decreased anchorage-independent growth and tumor growth in vivo. Finally, we identified PIK3CB as a direct molecular interactor of miR-1287-5p and a pheno-copy factor for miR-1287-5p. Finally, targeting PI3K-signaling pathway with chemical inhibitors together with miR-1287-5p mimics increased the pharmacological growth inhibitory potential.   Conclusion:   In conclusion, our data identified for the first time an involvement of miR-1287-5p in human BC and suggest a potential for therapeutic interventions in hardly to treat triple negative BC.

overall_design: three biological replicates of stably transduced SUM159 miR-1287-5p overexpressing cells or empty vector transducted cells as control cells

first: Daniela

last: Schwarzenbacher

first: Verena

last: Stiegelbauer

first: Stefanie

last: Cerk

first: Barbara

last: Pasculli

first: Beate

last: Rinner

first: Michael

last: Karbiener

first: Cristina

last: Ivan

first: Raffaela

last: Barbano

first: Hui

last: Ling

first: Annika

last: Wulf-Goldenberg

first: Anna-Maria

last: Pehserl

first: Jan

middle: B

last: Adiprasito

last: Rinnerthaler

first: Margit

last: Resel

first: Herbert

last: Stoeger

first: Thomas

last: Bauernhofer

first: Johannes

last: Haybaeck

first: Gerald

last: Hoefler

first: Stephan

last: Jan

first: Paola

last: Parrella

first: George

last: Calin


title: Cabergoline-treated lutein granulosa cells from polycystic ovarian syndrome (PCOS) patients exhibit higher transcriptomic response than cabergoline-treated controls

city: Valencia

first: Patricia

last: Diaz Gimeno

state: Valencia

address: Avenida Fernando Abril Martorell 106

department: Reproductive Genomics

country: Spain

institute: Fundacion IVI/Universidad de Valencia

summary:
This study assessed the transcriptomic profiles of lutein granulosa cells (LGCs) from women with and without PCOS using Affymetrix microarray chips to provide novel information about the molecular changes that occur in these cells when they are treated with a D2-ag (Cb2) and to assess the signal transduction pathways regulated by this treatment.
Transcriptomic analysis, using Affimetrix Human 1.0ST. GeneChip Microarray was functionally analyzed by Gene Set Enrichment Analysis (GSEA) and network modeling with system biology perspective.

overall_design: This is a paired design that compared no treatment to treatment with Cb2 using LGCs from non-PCOS (controls, n=3) and PCOS patients (n=3) selected according to the Rotterdam criteria. LGCs from each patient were cultured with or without Cb2. Groups were designated Cu: control untreated (n=3), Ct: control treated (n=3), Pu: PCOS untreated (n=3), and Pt: PCOS treated (n=3). Transcriptomic analysis was performed with the 12 samples and 4 extra technical replicates (n=16).

first: H

last: Ferrero

first: P

last: Díaz-Gimeno


title: Expresson of CD271 HIGH and LOW populations in melanoma cells during invasion

city: Zurich

first: Gaetana

last: Restivo

state: ZH

address: Winterthurerstrasse 190

department: Anatomy

institute: University of Zurich

summary:
Human engeneered skin carrying GFP positive melanoma cells  was transplanted in immunocompromised rats.
6 weeks after transplatation the engeenered skin was removed and GFP positive melanoma cells sorted for CD271 HIGH and LOW populations

overall_design:
2 rats were transplanted, the 2 tranplants were then dissected and cell isolated by digestion. Melanoma cells were sorted for GFP
Functional Genomic Center University of Zürich Switzerland for Affymetrix and data analysis

first: G

last: Kiowki

first: T

last: Biedermann


title: Agilent LncRNA and mRNA array data for xenograft tumor of TE-2 cells in the nude mice

status: Public on Sep 01 2017

city: Xian

first: Jiaji

last: Lin

address: No. 1. XinSi Road

department: Neurology

country: China

institute: Forth Military Medicial University

summary: Although dysregulation of histamine and its receptor 4 (H4R) were widely and frequently appears in digestive carcinomas and was correlated with their malignancy and tumor proliferation, its existence and function in the esophagus and esophageal squamous cell carcinoma (ESCC) were still known. In our present study, we explored the expression and function of H4R in ESCC samples and cell lines.  The results showed that H4R was overexpressed in poor differentiated ESCC samples and cell lines and correlated with median survival. H4R activation significantly not only blocked cell proliferation, cell cycle and invasion, but also induced the TE-2 xenograft inhibition and mice survival rate promotion. Mechanistic research demonstrated both metabolism (ACSS2) and non-metabolism (MAPK) related pathways were involved in H4R function, and H4R activation suppressed TGF-β1 via both above signaling. These findings firstly confirmed H4R overexpression in the esophagus cancer and its anti-tumor effects in the ESCC proliferation and invasion, which suggested that H4R was a potential target in therapy for ESCC.

overall_design:
Agilent arrays were performed according to the manufacturer's directions on RNA extracted from xenograft tumors of TE-2.
All animal procedures were performed following the National Animal Experimentation guidelines and were approved by the ethics committee of the Kunming General Hospital of Chengdu Military Region. All nu/nu mice were bred in aseptic conditions at a constant humidity and temperature with standard 12 h light-dark cycles and free access to drinking water and standard chow. TE-2 cells (1 × 107 in 100 mL of PBS) were suspended in a volume of 0.2 ml serum-free medium and injected subcutaneously into the hind flanks of the animals. At the end of the treatment, the nude rats were sacrificed and xenograft tumors were harvested for tumor volumes calculation (0.5 × length (mm) × width2 (mm2) as well as other experiments. When the subcutaneous tumors reached 20 mm3 (about 3 w), The mice were randomly assigned to one of the following four groups: (1) Vel group: nude mice received I.V. injections of vehicle (0.9% NaCl) once a day for 4 w; (2) 4MH group: nude mice received I.V. injections of 100 μM/kg H4R agonist 4MH once a day for 4 w; (3) JNJ group: nude mice received I.V. injections of 100 μM/kg H4R antagonist JNJ once a day for 4 w. Tissue samples and cells were put into liquid nitrogen for 10 min and then into an ultra freezer at 80°C. Total RNA was extracted using the GeneJET RNA purification Kit according to the manufacturer’s instructions (Thermo Scientific). RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis. Arraystar Mouse mRNA and LncRNA Microarray V3.0 is applied for the global profiling of mouse LncRNAs and protein-coding transcripts. About 35,923 LncRNAs and 24,881 coding transcripts can be detected by our third-generation mRNA and LncRNA microarray. Differentially expressed genes (DEGs) of 4MH group (between 100 μM/kg histamine H4 receptor agonist 4-methylhistamine treatment and control vehicle (0.9% NaCl) treatment) and JNJ group (between 100 μM/kg histamine H4 receptor antagonist JNJ7777120 and control vehicle (0.9% NaCl) treatment) were identified through the random variance model. A p-value was calculated using the paired t-test. The threshold set for up- and down-regulated genes was a fold change ≥ 2.0. The GO and pathway analysis were performed and the pain related GO terms were picked up for subsequent examination.

first: Jia-Ji

first: Wen-Ke

last: Cai


title: Expression data from HeLa cells upon interferon-gamma or interferon-beta treatment

city: Cambridge

first: Michal

middle: P

last: Wandel

address: Francis Crick Avenue, Cambridge Biomedical Campus

department: PNAC

institute: MRC Laboratory of Molecular Biology

summary:
Immune interferon beta and gamma are essential for mammalian host defence against intracellular pathogens.
We used microarrays to detail the global programme of gene expression upon interferon-gamma or interferon-beta treatment and identified distinct classes of up-regulated genes.

overall_design: HeLa cells were unstimulated or stimulated with interferons for RNA extraction and hybridization on Affymetrix microarrays.

first: Felix

last: Randow


title: Gene expression assessed by genome wide hybridization bead array in T84 polarized tight monolayers after challenge with celiac disease-associated bacteria and gluten [CTR glut bmix, bmix and gluten]

city: Umeå

first: Marie-Louise

last: Hammarström

address: Peter Lestadius väg

department: Clinical Microbiology

institute: Umeå universitet

summary: Analysis of the influence of celiac disease-associated bacteria and gluten on intestinal epithelial cells

overall_design: Stimulation with CD-associated bacteria and gluten was done from the apical side of polarized tight monolayers of T84 cells by replacing the medium in the upper chamber with 0.5 mL challenge medium containing 5x10^7 bacteria with or without 1 mg trypsin-treated gluten/mL. For each stimulant three parallel wells were used to carry out the experiment and wells treated with challenge medium only served as experimental controls. The challenge was done under anaerobic condition and at 37°C for 4 hours. The bacteria mix includes Prevotella jejuni (three isolates) + P. melaninogenica + P. histicola + Lachnoanaerobaculum umeaense + Actinomyces graevenitzii in ratio 1:1:1:1:1:1:1. Gluten = tryptic digest of wheat gluten.

first: Grzegorz

last: Pietz


title: CDK8 Mediator kinase drives colon cancer hepatic metastasis by regulating gene expression of the matrix metalloproteinase network [Affymetrix]

city: Columbia

first: Mengqian

last: Chen

state: SC

address: CLS710, 715 Sumter Street

department: College of Pharmacy

institute: University of South Carolina

summary: CDK8 Mediator kinase is amplified and overexpressed in colon cancers; elevated CDK8 expression is associated with shorter patient survival. Nevertheless, CDK8 kinase inhibitors do not generally suppress colon cancer growth. We addressed this paradox by investigating the effects of CDK8 knockdown or a CDK8 kinase inhibitor on tumor growth at primary and metastatic sites. CDK8 knockdown or inhibition had no significant effect on primary tumors but suppressed the growth of hepatic metastases in murine and human colon cancer models. The effect of CDK8 inhibition on liver metastasis is mediated by upregulation of matrix metalloproteinase (MMP) inhibitor TIMP3 and downregulation of several MMPs.

overall_design: Microarray analysis comparing CT26 cells treated with DMSO and 5 µM Senexin B for 24 h and the comparison between CT26-pLKO.1 and CT26-shCDK8 were performed using Affymetrix Mouse gene 2.0 X ST arrays by the Functional Genomics Core of the Center for Targeted Therapeutics at the University of South Carolina.

first: Jiaxin

last: Liang

first: Igor

last: Roninson


title: Depletion of Mob1a/b causes intestinal epithelia degeneration by suppressing Wnt and activating BMP/Tgfβ signaling

city: Seoul

first: June Sung

last: Bae

address: 31, Ttukseom-ro 1-gil, Seongdong-gu

country: South Korea

institute: SG Medical

summary: To investigate the cause of defects in intestinal epithelial cells (IECs) homeostasis and acute death of IECs specific Mob1a/b double knockout mice, microarray analysis with isolated IECs was performed.

overall_design: Gene expression in IECs was measured at 0, 4 and 7days after conditional knockout of Mob1a/b in 8 week old mice. IECs were isolated from proximal region of intestine using 2mM EDTA/PBS solution. This experiment was performed using two different male mice at each time (0, 4 or 7days).

first: Ho

last: Lee

first: June