title: Circadian misalignment induces fatty acid metabolism gene profiles and induces insulin resistance in human skeletal muscle.

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: Circadian misalignment, such as in shift work, has been associated with obesity and type 2 diabetes, however, direct effects of circadian misalignment on skeletal muscle insulin sensitivity and muscle molecular circadian clock have never been investigated in humans. Here we investigated insulin sensitivity and muscle metabolism in fourteen healthy young lean men (age 22.4 ± 2.8 years; BMI 22.3 ± 2.1 kg/m2 [mean ± SD]) after a 3-day control protocol and a 3.5-day misalignment protocol induced by a 12-h rapid shift of the behavioral cycle. We show that circadian misalignment results in a significant decrease in peripheral insulin sensitivity due to a reduced skeletal muscle non-oxidative glucose disposal (Rate of disappearance: 23.7 ± 2.4 vs. 18.4 ± 1.4 mg/kg/min; control vs. misalignment; p=0.024). Fasting glucose and FFA levels as well as sleeping metabolic rate were higher during circadian misalignment. Molecular analysis of skeletal muscle biopsies revealed that the molecular circadian clock was not aligned to the new behavourial rhythm, and microarray analysis revealed the human PPAR pathway as a key player in the disturbed energy metabolism upon circadian misallignement. Our findings may provide a mechanism underlying the increased risk of type 2 diabetes among shift workers.

overall_design: Microarray analysis was performed on skeletal muscle biopsies (m. vastus lateralis) from healthy lean young men in a circadian misalignment study.

first: Jakob

last: Wefers

first: Dirk

last: van Moorsel

first: Jan

last: Hansen

first: Sander

last: Kersten

first: Patrick

last: Schrauwen


title: Argonaute2 (Ago2) immunoprecipitation (IP) assay using miR-130b overexpressing A549 cells.

status: Public on Aug 09 2018

city: Suita

first: Kentaro

last: Jingushi

state: Osaka

address: 1-6 Yamadaoka

department: Graduate School of Pharmaceutical Sciences

country: Japan

institute: Osaka University

summary: To identify target genes of miR-130b in NSCLC cells.

overall_design: mRNA obtained from empty vector-transfected or miR-130b overexpressed A549 cells by Ago2-IP were analyzed for microarray.

first: Yuko

last: Ueda

first: Takayuki

last: Hirono


title: Repeated social defeat stress (R-SDS)-induced changes in gene expression profiles in microglia or whole medial prefrontal cortex

city: Kobe

first: Tomoyuki

last: Furuyashiki

state: Hyogo

address: 7-5-1, Kusunokicho, Chuo-ku

department: Pharmacology

institute: Kobe University Graduate School of Medicine

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

overall_design: Refer to individual Series


title: Rhesus macaque (Macaca mulatta) placental transcriptome

city: Cincinnati

first: Caitlin

middle: E

last: Dunn

state: Ohio

address: 3333 Burnet Avenue

department: Division of Human Genetics

country: USA

institute: Cincinnati Children's Hospital Medical Center

type: Expression profiling by high throughput sequencing

summary: The purpose of the experiment was to compare placental transcriptome of rhesus macaque at approximately 80% completed gestation to human placental transcriptomes.

overall_design: mRNA-seq from two rhesus macaque placentas at approximately 80% completed gestation

last: Dunn-Fletcher

first: Louis

middle: J

last: Muglia

first: Mihaela

last: Pavlicev

first: Suhas

last: Kallapur


title: Malignant canine mammary epithelial cells shed exosomes containing differentially expressed microRNA that regulate oncogenic networks

status: Public on Aug 13 2018

city: HUNTSVILLE

first: NRIPESH

last: PRASAD

state: AL

address: 601 GENOME WAY

department: GENOMIC SERVICES LABORATORY

institute: HUDSONALPHA INSTITUTE FOR BIOTECHNOLOGY

type: Non-coding RNA profiling by high throughput sequencing

summary: Breast (mammary) cancers in human (BC) and canine (CMT) patients share clinical, pathological, and molecular similarities that suggest dogs may be a useful translational model. Many cancers, including BC, shed exosomes that contain microRNAs (miRs) into the microenvironment and circulation, and these may represent biomarkers of metastasis and tumor phenotype. Three normal canine mammary epithelial cell (CMEC) cultures and 5 CMT cell lines were grown in serum-free media. Exosomes were isolated from culture media by ultracentrifugation then profiled qualitatively. CMEC and CMT cell lines shed round, “cup-shaped” exosomes approximately 150-200 nm by dynamic light scattering (DLS) and immunopositive for exosomal marker CD9 using Western blot. Exosomal small RNA was deep-sequenced on an Illumina HiSeq2500 sequencer and validated by qRT-PCR. Deep-sequencing averaged ~15 million reads/sample. 338 unique miRs were detected, with 145 having > ±1.5-fold difference between one or more CMT and CMEC samples. Gene ontology analysis revealed that the upregulated miRs in this exosomal population regulate a number of relevant oncogenic networks. Several miRNAs including miR-18a, miR-19a and miR-181a were predicted in silico to target the canine estrogen receptor (ESR1α). CMEC and CMT cells shed exosomes in vitro that contain differentially expressed miRs. CMT exosomal RNA expresses a limited number of miRs that are up-regulated relative to CMEC, and these are predicted to target biologically relevant hormone receptors and oncogenic pathways. These results may inform future studies of circulating exosomes and the utility of miRs as biomarkers of breast cancer in women and dogs.

overall_design: Exosomal microRNA profiled by small RNAseq in a case-control design between five canine mammary tumor (CMT) cell lines and three normal canine mammary epithelial cells (CMEC)

first: Eric

last: Fish

first: Richard

middle: C

last: Bird

first: Nripesh

last: Prasad

first: Kristopher

last: Irizarry

first: Connor

last: Ellis


title: The Effect of Maternal Care on Gene Expression and DNA Methylation in Ceratina calcarata

city: Griffin

first: Brendan

middle: G.

last: Hunt

state: GA

address: 125 Redding Building, Griffin Campus, 1109 Experiment Street

department: Entomology

institute: University of Georgia

type: Methylation profiling by high throughput sequencing

summary: Using a combination of Whole Genome Bisulfite Sequencing (WGBS) and RNA Sequencning (RNA-seq) we explored the effect that the loss of maternal care has on newly eclosed female offspring in the subsocial carpenter bee Ceratina calcarata.

overall_design: Mapping of 5-methylcytosine and quantification of gene expression in newly eclosed offspring raised in the presence or absence of maternal care

middle: G

first: Sandra

last: Rehan


title: Fibrostenotic phenotype of fibroblasts in Crohn's disease is dependent on tissue stiffness and reversed by LOX inhibition

city: Amsterdam

first: Jessica

middle: Rebecca

last: de Bruyn

address: Meibergdreef 69

department: Gastroenterology and Hepatology

institute: Academic Medical Center

summary: The results of this study indicate that stenotic fibroblasts exhibit an aberrant response to tissue stiffness with reduced MMP activity, leading to a perpetuous vicious circle of ever more fibrosis formation. Altering the microenvironment by LOX inhibition increases MMP activity and decreases ECM contraction, resulting in a potential anti-fibrotic agent for Crohn’s disease.

overall_design: Total RNA of human intestinal fibroblasts from 8 individual Crohn's disease patients. From every patient we used paired normal, inflamed and stenotic mucosa to isolate fibroblasts.

middle: R

first: Gijs

last: van den Brink

last: Steenkamer

first: Christianne

last: Buskens

first: Willem

middle: A

last: Bemelman

first: Sander

last: Meisner

first: Vanesa

last: Muncan

first: Anje

last: te Velde

first: Geert

last: D'Haens

first: Manon

last: Wildenberg


title: Diagnosis of Kawasaki Disease in children using host RNA expression [Validation_HT12V4_Dataset]

city: London

first: Michael

last: Levin

address: South Kensington Campus

department: Paediatrics

country: United Kingdom

institute: Imperial College London

summary: Genome-wide analysis of transcriptional profiles in children <17 years of age with inflammatory diseases, bacterial or viral infections or with clinical features suggestive of infection.

overall_design: Patients were recruited at or after presentation to hospital. Main inclusion criteria were presence of illness of sufficient severity to warrant blood tests for clinical reasons, in child aged <17 years. Blood was collected into PAX gene tubes (PreAnalytiX). Total RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA). Labeled cRNA was hybridized to Illumina Human HT-12 V4 Beadchips (Validation set HT-12 V4). Numbers of arrays analysed in the validation set were as follows: Kawasaki Disease Acute (n=146), Kawasaki Disease Convalescent (n=87).


title: Diagnosis of Kawasaki Disease in children using host RNA expression [Validation_HT12V3_Dataset]

overall_design: Patients were recruited at or after presentation to hospital. Main inclusion criteria were presence of illness of sufficient severity to warrant blood tests for clinical reasons, in child aged <17 years. Blood was collected into PAX gene tubes (PreAnalytiX). Total RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA). Labeled cRNA was hybridized to Illumina Human HT-12 V3 Beadchips (Validation set). Numbers of arrays analysed in the validation set were as follows: Kawasaki Disease (n=1), Healthy controls (n=16), Definite Bacterial infection (n=23), Definite Viral infection (n=28), infections of uncertain bacterial or viral aetiology (n=79).


title: Impact of Cugbp1 knockout on skeletal muscle and brain trancsriptome in neonatal mice

status: Public on Aug 08 2018

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

summary:
To elucidate the role of Cugbp1 knockout on the structure and function of skeletal muscle and brain, we have performed a microarray of mRNA obtained from skeletal muscle and brain samples obtained from neonatal WT and Cugbp1 KO mice.
Between-genotype differences were assessed using a Student's T-test, with a p-value cutoff of 0.05 and fold change cutoff of 1.5.  929 genes were identified as differentially regulated; ontological enrichments within this geneset indicated Cugbp1 may  regulate differentiation, extracellulat matrix and other muscle functions during myogenesis.

overall_design:
The impact of Cugbp1 knockout on the skeletal muscle and brain transcriptome was assessed through a microarray of mRNA obtained from skeletal muscle and brain samples in WT and Cugbp1 KO neonatal mice.

The submitter states that raw data are not available for this series.

first: Lubov

last: Timchenko


title: Gene expression profile of Endothelial colony-forming cells (ECFCs) isolated from patients with unprovoked venous thromboembolism (uVTE)

city: Rozzano

first: Domenico

last: Mavilio

address: Via Manzoni 113

department: Dept of Medical Biotechnologies and Translational Medicine

country: Italy

institute: University of Milan - Humanitas Clinical and Research Center

summary: Anlysis of ECFCs isolated from uVTE patients at gene expression level. The hypothesis tested in the present study was that endothelial dysfunction could be involved in uVTE pathogenesis. Results provide important information on endothelial compartement of uVTE patients identifying either significantly up- and down regulated genes.

overall_design: Total RNA obtained from ECFCs obtained from uVTE patients compared to ECFCs obtained from healthy controls.

first: Silvia

last: Della Bella

first: Francesca

last: Calcaterra

first: Monica

last: Bacci

first: Claudia

last: Carenza

first: Chiara

last: Pandolfo

first: Paola

last: Ferrazzi

first: Paolo

last: Uva

first: Massimiliano

last: Pagani

first: Corrado

last: Lodigiani


title: Differences among inbred mouse strains in sensitivity to TGF-ß1 induced renal fibrosis: association with TIMP-1 and EGR2 expression

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

summary:
Alb/TGF-ß1 (TGF-ß) transgenic mice on mixed (CBAxB6) genetic background are characterized by renal fibrosis with mild or severe phenotype. Our aim was to examine the influence of genetic background on TGF-ß induced renal fibrosis in transgenic mice, and to elucidate the molecular details of strain dependent progression of fibrosis.
We generated congenic B6-TGFß transgenic mice and CBAxB6-TGFß transgenic hybrid mice. Survival, proteinuria, renal histology, renal transcriptome using cDNA microarray and protein expression were analysed.

overall_design: B6-TGFß (WT) and CBAxB6-TGFß (KO) kidneys were analyzed (n=3/group).

first: Gábor

last: Kökény

first: Lilla

last: Fang

first: Jeffrey

middle: B

last: Kopp

first: Weiping

first: Andrew

last: Oler

first: Péter

last: Hamar

first: László

last: Rosivall

first: Miklós

middle: M

last: Mózes


title: Expression data of ECa9706 over expressing miR-144/451 cluster

city: Nanjing

first: Zhikui

last: Gao

address: 87# Dingjiaqiao Road

country: China

institute: Southeast University

summary:
miR-144/451 cluster is highly conversed in different species, miRbase database  shows miR-144/451 cluster is constituted by miR-144-3p, miR-144-5p, miR-451a. Low-expression of miR-144/451 was closely related with the risk for esophageal cancer
We used microarrays to identify the differentially expressed genes in ECa9706 over expressing miR-144/451 cluster

overall_design: To obtain pri-miR-144/451 cluster plasmid, a synthetic sequence within the range of upstream 200bp to downstream 200bp of pri-miR-144/451 was cloned into the PCDH-CMV-MCS-EF1-Puro lentivirus plasmid. Plasmids of pMDLg/Prre, pRSV-Rev, pMD2G and PCDH-CMV-MCS-EF1-Puro were transfected into HEK-293T for packaging lentivirus. We detected the expression of genes in cells overexpressing miR-144/451 cluster (A9547, A9548 and A9549) and the control (A9546, A9547 and A9548).

first: Ran

last: Liu


title: Gene expression profile of FMR1-KO iPSCs-derived NPCs

status: Public on Aug 07 2018

first: Kei

last: Enomoto

address: Chuo-ku, Minatojima-Minamimachi

institute: ASUBIO PHARMA CO., LTD.

summary: Fragile X syndrome (FXS) is caused by transcriptional silencing of the FMR1 gene during embryonic development with the consequent loss of the encoded fragile X mental retardation protein (FMRP). The pathological mechanisms of FXS have been extensively studied using the Fmr1-knockout mouse, and the findings suggest important roles for FMRP in synaptic plasticity and proper functioning of neural networks. However, the function of FMRP during early neural development in human nervous systems remains to be confirmed. We established human neural progenitor cells (NPCs) as a model for studying FMRP functions and FXS pathology. In order to identify the differentially expressed genes in FMR1KO-NPCs, we performed DNA array analysis on this model.

overall_design: We disrupted FMR1 gene in a male induced pluripotent stem cells (iPSCs) line TIG114 using gene editing. Resultant iPSCs were then differentiated into NPCs. DNA array analysis were performed on NPCs derived from FMR1-KO iPSC line (iNPC-KO) and the parental line (iNPC-WT). Duplicate for each genotypes were analyzed (4 samples in total).


title: FGF4 is a target of EWS-OCT-4 in Embryonic stem cell

city: SEOUL

first: JUNG

middle: HOON

last: KIM

state: MAPOGU

address: SOGANG R 1206

department: LIF SCIENCE

country: South Korea

institute: SOGANG UNIV

summary: FGF4 has key role in self-renewal and differentiation of Embryonic stem cell, and Fgf4 is activated by direct binding of ESW-OCT-4 through its enhancer

overall_design: we used Niwa-GFP stable cell line as control group, and Niwa EWS-OCT4A-GFP stable cell line as an experimental group.  All experiments are duplicated.

first: Jung-Hoon

last: Kim

first: Hyo-Sun

first: Jung-Ho


title: GATA4 silenced HUH6 hepatoblastoma cells

status: Public on Aug 06 2018

city: Helsinki

first: Tea

last: Soini

address: Biomedicum 2U, Tukholmankatu 8

department: Children's Hospital

country: Finland

institute: University of Helsinki

summary: The effects of GATA4 silencing on global gene expression in HUH6 hepatoblastoma cells was analyzed. Using microarray analysis we identified a set of genes that are downregulated or upregulated following silencing of GATA4 in HUH6 cell line.

overall_design: HUH6 cells were transfected with non-targeting (NT) control siRNA and GATA4 siRNA (n=6 in each sample group). 72h post transfection cells were lysed and RNA was extracted.

first: M

last: Heikinheimo

first: T

first: O

last: Akinrinade

last: Pihlajoki

first: K

last: Eloranta


title: mRNA Expression data from murine hearts subjected to ligation of the left anterior descending coronary artery (myocardial infarction, MI model) or sham surgery (SH)

city: Guelph

first: Elena

last: Tsimakouridze

address: 50 Stone Rd E

country: Canada

institute: University of Guelph

summary:
The left anterior descending coronary artery permanent ligation model of myocardial infarction was used to study the time of day differences in genetic responses post-MI  between sleep-time MI, wake-time MI, wake-sham and sleep-sham mouse hearts.
The micorarray approach allows the investigation of gene expression changes of all genes in sleep-time MI vs. wake-time MI vs. sham hearts.

overall_design: There are a total of 12 samples, 6 from cardiovascular disease MI and 6 from normal SHAM hearts collected 8 hours after surgery. Specifically for MI: There were 3 mice sacrificed 8 hours after wake-time MI as biological replicates, and there were 3 mice sacrificed 8 hours after sleep-time MI as biological replicates. Specifically for SHAM: There were 3 mice sacrificed 8 hours after wake-time SH as biological replicates, and there were 3 mice sacrificed 8 hours after sleep-time SH as biological replicates.

first: Tami

last: Martino


title: Transcriptional dysregulation of inflammatory/immune pathways after active vaccination against Huntington’s disease

city: Albany

first: Andrew

middle: Arthur

last: Reilly

state: NY

address: 150 New Scotland Ave

department: Genetics

institute: Wadsworth Cntr, NYS Dept of Health

summary: Transcriptome profiling of spleens from the triple peptide-immunized cohort showed substantial HD-specific differences including differential activation of genes associated with innate immune responses, absence of negative feedback control of gene expr

overall_design: HD R6/1, zQ175 and +/+ mice were immunized with a combination of 3 peptides from HTTExon1. Spleens were collected 10 days after final boost. Transcriptome was determined by Affimetrix chip. Data analyzed by GSEA.

first: Arlene

middle: I

last: Ramsingh

first: Kevin

last: Manley

first: Anne

last: Messer


title: Expression data from Py117 and Py8119 cancer cell lines and Tumors

city: Dallas

first: Todd

last: Aguilera

state: TX

address: 2280 Inwood Rd

department: Molecular radiation biology

institute: UTSouthwestern- Medical Center

summary:
To investigate the impact of tumors cloness on the immune microenvironment using immunologically responsive and unresposive clones.
we used mixed population of immunologically responsive and unresponsive tumor clones in different ratios for their response to irradiation (RT). We found that the response to RT was influenced by even a small number of immune responsive cells

overall_design: Tumor cell lines with heterogeneous immune responses to radiation that were derived from the PyMT genetically engineered mouse model of mammary carcinoma and analysis of the microevironmental factors and immunologic responses generated by sensitive Py117 tumor clones and resistant Py8119 clones within the same microenvironment

first: Amato

last: Giaccia


title: Arabidopsis thaliana wild type and PDKO3 mutant mechanical damage (MD) vs herbivore wounding (HW)

status: Public on Aug 05 2018

city: Turin

first: Cinzia

middle: Margherita

last: Bertea

state: To

address: via Quarello 11/A

department: Department of Life Sciences and Systems Biology

institute: University of Turin

summary: Transcriptional profiling of Arabidopsis thaliana wild type (WT) and a line mutated in genes encoding plasmodesmata (PD) proteins (PDKO3) comparing MD (mechanical damage) and HW (herbivore wounding). The differences in the biochemical responses to herbivory seen in the PDKO3 when compared to the WT line, together with the absence of growth/developmental phenotypes in the former, prompted us to search for less obvious differences between the lines using gene expression profiling.

overall_design: Two-condition experiment, MD vs. HW Arabidopsis leaves of two different lines WT and PDKO3. Biological replicates: 3 biological replicates for each condition. Additionally for two of the samples, 3 technical replicates were applied.

first: Massimo

last: Maffei

first: Ivan

last: Paponov

first: Yong

last: Li


title: Transcriptomic analysis of SKM1 cells treated with APR-246 (APR), 5-Azacytidine (AZA) or both (APR-AZA)

status: Public on Aug 04 2018

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

country: France

institute: INSERM

summary: In order to explain the synergistic effects observed by the combination APR+AZA in MDS cells by synergistic activated pathways, we performed a transcriptomic analysis of MDS cells treated with each drug alone and compared it to the combination.

overall_design: Triplicates of SKM1 cells were submitted to IC50 of APR or IC50 of AZA alone or in combination and compared to untreated control. RNAs were extracted after 18h of culture.

first: Stéphane

last: Giraudier

first: Nabih

last: Maslah


title: Comparative expression data between intestinal epithelium of FSPCre-PPARB -/- and PPARB flox/flox

city: Singapore

first: Eddie

middle: Han Pin

last: Tan

address: 60 Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

summary:
Stroma secretes a multitude of regulatory signals that are involved in mediating intestinal development. Ablation of PPARB expression in fibroblastic cells results in modulation of oxidative stress signals that lead to altered intestinal morphology and gene expression profiles
Through gene chip expression profiling, we seek to identify key changes in intestinal mucosal gene expression profiling between FSPCre-PPARB flox/flox and PPARB flox/flox mice.

overall_design:
Expression profiling of FSPCre-PPARB KO colon mucosa, FSPCre-PPARB KO ileum mucosa, PPARB floxed colon mucosa, PPARB floxed ileum mucosa.
Intestines were harvested from 4 to 6 week old C57BL6/J mice and prepared for histological staining. Intestinal mucosal tissue were microdissected from stained histological slides using Zeiss PALM III laser disection microscope.

middle: H

first: Chek

middle: K


title: Gene expression study of human endometrial receptivity in IVF implantation failure patients undergoing ovarian stimulation

city: Mumbai

first: Indira

last: Hinduja

address: 15, Dr. G. Deshmukh Marg

country: India

institute: Jaslok Hospital and Research centre

summary: Endometrial receptivity on genomic level is one of the major cause of implantation failure in IVF patients with unexlained infertility and is a main obstacle in success of IVF. Gene expression profiles of implantation failure cases of unexplained infertility were compared with proven healthy oocyte donors as controls, both undergoing ovarian stimulation. The results provide additional information about gene expression profile related to endometrial receptivity in implantation failure cases especially under the influence of ovarian stimulation during IVF cycle.

overall_design: Total RNA isolated from endometrial tissue collected during implantation window from implantation failure cases with unexplained infertility (having normal hormones and endometrium with 8 mm and above, triple layered) were compared with oocyte donors as healthy proven fertile controls under the influence of long protocol of ovarian stimulation during IVF.

first: Amruta D

middle: S

last: Pathare

first: Manisha

last: Chaudhari-Kank

first: Kusum

last: Zaveri


title: Evidences of a MYC-driven precursor-B cell acute lymphoblastic leukemia (ALL) arising in the zebrafish rag2:hMYC T-cell ALL model

city: Padova

first: Chiara

last: Borga

address: Corso Stati Uniti,4

institute: University of Padua

summary: GFP+ leukemia arising in young adult zebrafish (6 month) were FACS-purified for RNA extraction and hybridization on Affymetrix microarrays. Two zebrafish ALL models included in this study, hMYC;GFP and hlk line, to investigate differences and similarities of leukemia arising in animals with different genetic background.

overall_design: Gene expression profiling of GFP+ Acute Lymphoblastic Leukemia (ALL) FACS-purified from 10 hMYC;GFP and 3 hlk individual fish.

first: Geertruy

last: Te Kronnie


title: Modeling Malignant Bone Disease Using Microgravity Bioreactors, Genetically Engineered Cell Lines, Patient-Derived Tumor Xenografts and Stem Cells

city: Temple

first: Carl

last: Gregory

state: Texas

address: 5701 Airport Road

department: Molecular and Cellular Medicine

institute: Texas A&M Health Sciences Center

summary: Transcriptome data from mesenchymal stem cells cultured in osteogenic conditions on monolayers of microcarriers coated with collagen I or extracellular matrix derived from osteogenically enhanced human mesenchymal stem cells (hereafter referred to as hMatrix)

overall_design: Two million GFP-labeled hMSCs were attached to collagen I- or ECM-coated beads with a combined growth area of 50 cm2. The loaded beads were then suspended in 10 mL of CCM and transferred into the RWV culture system. After 48 hours of equilibration, the CCM was removed and replaced with OEM so as to generate OEhMSCs. The cultures were incubated for 8 days with changes of media every 2 days. Triplicate cultures for collagen-I coated and ECM coated beads were performed. After 8 days, the cell-laden beads were recovered by brief centrifugation, washed in PBS and subjected to total RNA purification. Resultant total RNA yields ranged from 4.5-13.5 ug at a concentration of 150-450 ug mL-1 with OD260/280 ratios ranging from between 1.85-2.0. Thereafter, sample preparation and data acquisition was performed by the UT Southwestern Genomics and Microarray Core Facility. RNA integrity was confirmed by analysis using an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA) and RNA integrity scores were 10 in each case. Biotin-UTP labeled antisense copy RNA (cRNA) was generated from 200 ng of total RNA using a commercially available kit (Illumina TotalPrep RNA Amplification Kit, Life Technologies, Carlsbad, CA). Labeled cRNA was hybridized to a HumanHT-v4.0 Expression BeadChip (Illumina, San Diego, CA) and visualized with biotin-Cy3 (Amersham, Piscataway, NJ, USA). Chips were read on an Illumina Hiscan scanner and analyzed according to standard manufacturer’s protocols using GenomeStudio version 3 (Illumina). Background correction, quality control, and quantile normalization were performed in accordance with Illumina standard operating procedures. Mean normalized fluorescent intensities and standard deviations were calculated for each transcript using biological triplicates for each condition. Data for a given transcript were excluded if the standard deviations exceeded 0.25 of the mean. Linear fold changes were calculated between type I collagen and ECM coatings using mean intensity values and lists were compiled of those genes that were upregulated by 2 fold or higher.


title: Distribution of chromatin features in mouse P19 embryonal carcinoma cells

status: Public on Aug 03 2018

city: Glasgow

first: Katherine

last: West

address: University of Glasgow

department: College of Medical, Veterinary and Life Sciences

institute: University of Glasgow

type: Genome binding/occupancy profiling by high throughput sequencing

summary: CHIP to investigate Hmgn2 binding in P19 undifferentiated and differentiated neuronal cells.

overall_design: ChIP seq was performed for Hmgn2, H3K27ac, H3K4me1, H3 and IgG in undifferentiated P19 cells and in cells differentiated down the neuronal lineage for three days.

middle: L


title: MeDIP Sequencing for 2 rat liver Samples

city: Chongqing

first: XINYU

last: LI

address: 1 YOUYI ROAD

institute: The First Affiliated Hospital of Chongqing Medical University

summary: Diabetes exerts adverse effects on the initiation or progression of diabetes and metabolic syndrome of in the next generation. In past studies, limited attention has been given to the fathers’ role in shaping the metabolic landscape of offspring. Our study was designed to investigate how paternal hyperglycemia exerts an intergenerational effect in mammals as well as the underlying mechanisms. Hyperglycemia was introduced in male rats by intraperitoneally injected streptozotocin and these males were bred with healthy female rats to generate offspring. The metabolic profiles of the progeny were assessed, and DNA methylation profiles as well as gene expression related to lipid metabolism were investigated.

overall_design: Examination of methylation status on the offspring of male rats treated with streptozotocin and citrate buffer,anaysis of 1 sample for each group was completed.

first: Xinyu

first: XiaoQiu

last: Xiao


title: Genome-wide profiling of siRNA targeting PRKDC in Ewing sarcoma and non-Ewing sarcoma cell lines

first: Suntae

last: Kim

address: Bldg 37, room 6128

department: Genetics Branch

institute: CCR, NCI, NIH

summary: Identification of genes and pathways that were influenced by knock-down PRKDC in TC32 Ewing sarcoma and HCT116 colorectal carcinoma cell lines.

overall_design: TC32 Ewing sarcoma and HCT116 colorectal carcinoma cell lines were transfected with control siNeg or siRNA corresponding PRKDC gene. Three samples in each group were analyzed.

first: Sen

last: Nirmalya

first: Natasha

last: Caplen


title: Genome-wide profiling of Ewing sarcoma cell lines with nu7441 treatment

summary: Identification of genes and pathways that were influenced by nu7441, the PRKDC inhibitor, in Ewing sarcoma cell lines.

overall_design: TC32 and SKNMC Ewing sarcoma cell lines were treated with 0.1% (v/v) DMSO vehicle or 40 µM nu7441 in 48 hours. Three samples in each group were analyzed.


title: PRKDC, the catalytic subunit of DNA-dependent protein kinase, regulates EWS-FLI1 stability

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

overall_design: Refer to individual Series


title: EVI1 in acute myeloid leukemia triggers metabolic reprogramming associated with leukemogenesis

city: Miyazaki

first: Yusuke

last: Saito

address: 5200 Kihara Kiyotake-cho

institute: University of Miyazaki

summary: Overexpression of Ecotropic Virus Integration site 1 protein homolog (EVI1) in adults and children with mixed lineage leukemia-rearrangement acute myeloid leukemia (MLL-r AML) has a very poor prognosis. We used an extracellular flux analyze to examine metabolic changes during leukemia development in a mouse model of MLL-r AML expressing high levels of Evi1 (Evi1+).

overall_design: Two groups analyzed: 1) Whole MLL-AF9 leukemia cells from WT mice, 2) Whole MLL-AF9 leukemia cells from Evi1 Tg mice.

first: Y

first: H

last: Moritake


title: Glyoxalase 1 Knockout Promotes Age- and Sex-dependent Obesity and Metabolic Dysfunction

city: Los Angeles

first: Xia

last: Yang

state: CA

address: 610 Charles E Young Dr East

institute: UCLA

summary: Glyoxalase 1 (Glo1) is a critical enzyme responsible for the clearance of toxic dicarbonyls, which modify proteins to produce advanced glycation end products (AGEs). Glo1 has been recently implicated in the progression of metabolic disorders, however underlying mechanisms are poorly understood. We aim to investigate the role of Glo1 in metabolic perturbations and determine whether AGEs mediate the Glo1 activities in obesity and metabolic health.

overall_design: Total RNA obtained from the gonadal adipose, aorta, kidney and liver tissue from 36 weeks old female Glo1 heterozygous knockout (Glo1+/-) mice (n=3/group), compared with wild type mice at the same age.

first: Shu

last: Le

first: Qi

last: Hannah

first: Wu

last: Xiuju


title: Staphylococcus aureus gene expression during infection and antibiotic treatment with moxifloxacin in a guinea pig biofilm infection model

status: Public on Aug 02 2018

city: Aalborg East

first: Yijuan

last: Xu

address: Fredrik Bajers vej 7H

department: Department of Chemistry and Bioscience

country: Denmark

institute: Aalborg University

summary: Staphylococcus aureus is a major agent in device related infections. Upon infection, it upregulates virulence factors and adapts to host environment. We investigated the gene expression profile of S. aureus in a guinea pig infection model. Four Teflon® cages were placed subcutaneously in each of 12 animals prior to inoculation of a S. aureus strain from a patient with prosthetic joint infection (PJI). The animals were divided into two groups of six, one treated with moxifloxacin after three days of infection and for four days, and the other untreated. Cage fluid and cages were collected for RNA sequencing analysis and metabolomics. The gene expression profiles in untreated controls on day 7 and 9 were not differentiable and resemble the profile reported for the PJI case from where the strain originated. Compared to the profiles from day 3, we found upregulation of ammonia production through urea degradation, arginine deiminase and acetoin biosynthesis pathways on day 7 and 9, while several virulence genes were downregulated. Interestingly, the transcriptome seven day after termination of moxifloxacin treatment resembled infection day 3.  Overall, the gene expression profiles showed adaptation to hypoxic and acidic environment during infection development. We deem the model to be suitable for pathogenesis studies.

overall_design: Staphylococcus aureus differential gene expression during infection development in a guinea pig infection model. Twelve animals were divided into two groups of six, one treated with moxifloxacin after three days of infection and for four days, and the other untreated. Cage fluid and cages were collected on infection day 3, 7, 9 and 14 for RNA sequencing analysis and metabolomics.

first: Lone

last: Larsen

first: Kåre

last: Nielsen

first: Henrik

middle: C

last: Schønheyder

first: Rene

last: Duus

first: Reinhard

last: Wimmer

first: Trine

last: Thomsen


title: Temporal analysis of physiological and transcriptome responses during high light exposure that lead to dynamic acclimation in Arabidopsis

city: Colchester

first: Philip

middle: Mark

last: Mullineaux

address: Wivenhoe Park

institute: University of Essex

summary: The photosynthetic capacity of mature leaves increases upon exposing plants to continuous or intermittent high light (HL). This is termed dynamic acclimation, which is an important determinant of plant productivity. We hypothesized that genes coding for transcription regulators (TRs), which respond rapidly (≤1h) and transiently to HL, initiate dynamic acclimation. To find such genes, a highly replicated time series transcriptomic dataset was generated from leaf 7 of low light (LL)-grown Arabidopsis thaliana plants subjected to HL for up to 6h. This revealed 3844 HL-responsive differentially expressed genes (DEGs). 49 transiently HL-induced TR DEGs were selected for Bayesian modeling, which revealed that B-BOX TRANSCRIPTION (CO) FACTOR32 (BBX32) was the most connected gene in an inferred network. Dynamic acclimation was elicited in Arabidopsis Col-0 by exposure to daily 4h HL over 5 days. Using this procedure on over-expressing (OE) and null mutant plants, it was shown that BBX32 is a negative regulator of dynamic acclimation. The same modeling connected BBX32 to the TR gene LONG HYPOCOTYL5 (HY5), but unlike BBX32, HY5 was shown to positively regulate dynamic acclimation. The severely diminished response to daily HL of BBX32–OE/hy5 plants suggest that in wild type plants, BBX32 and HY5 exert a balanced, flexible and complete regulation of dynamic acclimation.

overall_design: A novel experimental design strategy (A Mead et al, in preparation), based on the principle of the loop design, was developed to enable efficient extraction of information about key sample comparisons using a two-color hybridization experimental system. With 100 distinct samples (four biological replicates, at each of 12 time points in control low light (LL) conditions and high light (HL) conditions plus 4 biological replicate time zero samples) to be compared, the experimental design included 200 two-color microarray slides, allowing four technical replicates of each sample to be observed. One third of the slides were devoted to assessment of changes in gene expression between time points, using a simple loop design to link samples from time points across the sampled times, directly comparing samples collected on adjacent sampling times (i.e. Time zero with 0.5h HL, 0.5h HL with 1h HL, etc.). With the remaining slides, four separate loops were constructed comparing treatments, biological replicates and sampling times.

first: Ruben

last: Alvarez-Fernandez

first: Christopher

last: Penfold

first: Igor

last: Chernukhin

first: Dafyd

middle: J

last: Jenkins

first: Laura

last: Bowden

first: Jonathan

middle: D

last: Moore

first: Andrew

last: Mead

first: Phillip

last: Davey

first: Jack

last: Matthews

first: David

last: Rand

first: James

last: Beynon

first: Vicky

last: Buchanan-Wollaston

first: Neil

last: Baker

last: Wild

first: Katherine

last: Denby

first: Tracy

last: Lawson

first: Ulrike

last: Bechtold


title: OsCPK21 regulates rice pollen development

city: Beijing

first: Shenghua

last: Jia

address: No. 19, XinJieKouWai St., HaiDian District

institute: Beijing Normal University

summary: To identify the molecular mechanism of OsCPK21 regulating pollen development, a genome-wide analysis of the gene expression profiles in the rice spikelet of ZH11 and OsCPK21-RNAi transgenic plants during anther development was performed. Hybridization with the microarray and subsequent analysis showed that a total of 5020 genes displayed altered expression (at least 2-fold) under suppressed OsCPK21 expression. Among the altered genes, 1419 were up-regulated, and 3601 were down-regulated.

overall_design: The ZH11 and OsCPK21-RNAi (3 lines) plants were growth in the same condition. Then rice spikelets at stage 9 and 12 of anther development were chose and collected, and total RNA was extracted and amplified from these four samples.

first: Shengcheng

last: Han

first: Yingdian

last: Wang


title: Transcriptome comparison of cartilage from patients with and without osteoarthritis

city: St. Louis

first: Muhammad Farooq

last: Rai

state: MO

address: 660 S. Euclid Ave.

department: Orthopaedic Surgery

institute: Washington University School of Medicine

summary: Objective: To assess the impact of osteoarthritis (OA) on the transcripts and biological process in the articular cartilage between patients with and without OA.   Design: Patients undergoing arthroscopic partial meniscectomy (APM) without any evidence for OA and patients undergoing total knee arthroplasty (TKA) due to end-stage OA were consented. Healthy-appearing cartilage was garnered from the non-weight bearing site of the medial intercondylar notch. RNA preparation was subjected to SurePrint G3 human 8X60K RNA microarrays to probe differentially expressed (DE) transcripts followed by computational exploration of underlying biological processes and pathways. Real-time PCR was performed on selected transcripts to validate microarrays data.  Results: We identified 603 transcripts significantly (FDR <0.05) differentially expressed (293 elevated, 310 repressed) between APM and TKA samples (1.5 fold).  Among these, CFD, CSN1S1, TSPAN11, CSF1R and CD14 were the most prominent transcripts elevated in TKA group, CHI3L2, MEG3, HILPDA, COL3A1, COL27A and FGF2 were most highly repressed in TKA samples. Few long intergenic non-coding RNAs (linRNAs), and small nuclear RNAs (snoRNAs) were also differentially expressed between the two groups.  Conclusions: Numerous transcripts with potential relevance to the pathogenesis of OA are DE in OA and non-OA cartilage. These data suggest an involvement of metabolic signaling and epigenetic markers (lincRNAs, snoRNAs) in cartilage.

overall_design: We used Agilent microarrays to identify gene transcripts differentially expressed in cartilage tissues obtained from 12 patients with osteoarthritis and from 12 patients without osteoarthritis (arthroscopic partial meniscectomy). P4-010, P4-012, P4-104, and P4-108 were excluded from the final analysis.

first: Muhammad

middle: F

first: Lei

last: Cai

first: Eric

last: Tycksen

first: Robert

last: Brophy


title: Bacillus thuringiensis stains induced systemic resistance in Brassica napus L.

first: Lili

last: Geng

address: Hiandian district, Yuanmingyuan West road No.2

institute: Institute of Plant Protection, Chinese Academy of Agricultural Sciences

summary: Bacillus thuringiensis has insecticidal activity against a variety of important agricultural pests and exhibits good bacteriostatic resistance to a variety of plant pathogens, and recentily study have shown that two strains of Bt (B88-82 and RG1-6 Strain) can induce the tomato to produce resistance to R. solanacearum. However, only the induced signal pathway has been studied, and its active substances are not reported. The aim of this study was to further explore the Bt strain that could induce plant disease resistance and study the induced activity of the Bt strain, and to study the signal pathway induced by transcriptional sequencing and fluorescence quantitative PCR.  The results showed that there were 303 differentially expressed genes in rape after induction of 4F5 strain, among which 86 genes were up-regulated and 217 genes weredown-regulated. The result of 4BM1 strain induction was induced by transcriptase sequencing. There were 126 differentially expressed genes in rape. Among which 64 genes were up-regulated and 62 genes were down-regulated. The analysis of these differentialexpression genes revealed that they contained Salicylic acid pathway and Ethylene pathway-related genes, which need to be further verified.

overall_design: Brassica napus L were treated with Bt strain 4F5, 4BM1, and stilled water as control.  B. thuringiensis inoculum, the final density was 7.5×109 cfu, was sprayed on the root of 6-week-old rapeseed plants. The same volume of distilled water (DW) treatment as control. Five days after induction, rapeseed leaves were collected. For each treatment, 3 rapeseed seedlings were used.

first: M

first: L


title: Genome-wide distribution of two histone modifications, H3K4me3 and H3K27me3, in soybean embryos and seedlings

city: Davis

first: John

last: Harada

address: One Shields Avenue

department: Plant Biology

institute: University of California

summary: In this study, we examined the genome-wide deposition of two opposing histone modifications H3K4me3 and H3K27me3, in mid-maturation (stage B1) soybean embryos.

overall_design: Distribution of two histone modifications, H3K4me3 and H3K27me3, in soybean cotyledon, early , mid and late maturation stage embryos and 8 day post-imbibition seedlings.  For each developmental stage, ChIP for each histone modification, as well as H3-associated chromatin (control) were obtained for two biological replicates.  A total of 30 samples were sequenced using the Illumina HiSeq2000 platform.

first: Julie

last: Pelletier

first: Russell

last: Baden

last: Golberg


title: Genome-wide profiling of HCT116 colorectal carcinoma cell line with nu7441 treatment

city: Bethesda

first: Suntae

last: Kim

summary: Identification of genes and pathways that were influenced by nu7441, the PRKDC inhibitor, in HCT116 colorectal carcinoma cell line.

overall_design: HCT116 colorectal carcinoma cell lines were treated with 0.1% (v/v) DMSO vehicle or 40 µM nu7441 in 48 hours. Three samples in each group were analyzed.

first: Sen

last: Nirmalya

first: Natasha

last: Caplen


title: RNA-seq analysis of equine tenocytes exposed to siRNA targeting scleraxis (Scx) to identify novel targets of Scx-mediated mechanotransduction

city: Blacksburg

first: Linda A

last: Dahlgren

state: Virginia

address: Phase II Duck Pond Drive

department: Large Animal Clinical Sciences

institute: Virginia Tech

summary: Equine tenocytes were exposed to an siRNA targeting the transcription factor scleraxis (Scx) or a scramble control and maintained under cyclic strain. The resulting transcriptomes were then used for RNA-seq analysis. The goal of this study was to identify novel ways in which Scx facilitates mechanotransduction in tenocytes in order to better understand tenocyte biology.

overall_design: Transcriptomes of equine tenocytes with or without scleraxis (Scx) knockdown by siRNA were generated in triplicate.

first: Anne

middle: E

last: Nichols

last: Settlage

first: Stephen

middle: R

last: Werre

first: Linda

middle: A


title: RNA-seq analysis of transcriptome profile of Chlamydomonas reinhardtii exposed to silver nanoparticles

city: beijing

first: songshan

last: Wang

address: baiwanzhuang 11#

institute: ASAG

summary: The transcriptome of Chlamydomonas reinhardtii was characterized via RNA sequencing (RNA-seq) after exposure to a non-toxic concentration of AgNPs (0.05 mg/L). The copper deficiency responsive genes were discovered to be upregulated and responsible for the interaction between algae and  AgNPs.

overall_design: mRNA profiles of 2h and 12h of  algae exposed to AgNPs and the control check were generated by RNA sequencing using Illumina HiSeq™ 2500 platform

first: Songshan

first: Shuzhen

last: Zhang


title: Morphological profiling of chondrogencially-induced multipotent stromal cell aggregates reveals emergent morphological phenotypes predictive of functional capacity

status: Public on Aug 01 2018

city: Silver Spring

first: Ian

last: Bellayr

state: Maryland

address: 10903 New Hampshire Ave

institute: FDA

summary: Gene expression microarrays were used to determine gene expression differences between mesenchymal stem cells (MSC) from different donors and passage for their potential to undergo chondrogenic differentiation.

overall_design: Eight MSC cell lines at an early and late passage was hybridized to microarrays for a total of 16 different samples

first: Johnny

last: Lam

first: Ross

last: Marklein

first: Steven

last: Bauer

first: Raj

last: Puri

first: Kyung

last: Sung


title: Adam12 and lnc015192 act as ceRNAs in breast cancer by regulating miR-34a

city: Guangzhou

first: Xiaojia

last: Huang

address: 651 East Dongfeng Road

institute: Sun Yat-sen University Cancer Center

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

summary: Long non-coding RNAs (lncRNAs) are involved in the pathology of various tumors. However, the role of lncRNA in breast cancer remains unclear. We performed microarrays to identify the differentially expressed mRNAs and lncRNAs in breast tissues with or without miR-34a knockout. In vitro and in vivo assays were preformed to explore the biological effects of the differentially expressed mRNA and lncRNA in breast cancer cells. We found that Adam12 and lnc015192 were significantly upregulated in miR-34a knockout breast tissues. Knockdown of Adam12 and lnc015192 inhibited breast cancer cells migration, invasion and epithelial-mesenchymal transition (EMT) in vitro and in vivo. Further study indicated that lnc015192 acted as a competing endogenous RNA (ceRNA) for miR-34a to regulate Adam12 expression. Taken together, our findings demonstrate how Adam12 and lnc015192 induce breast cancer metastasis and offer novel therapeutic targets for breast cancer.

overall_design: We performed microarrays to identify the differentially expressed mRNAs and lncRNAs in female mice breast tissues with or without miR-34a knockout.

first: Xinhua

last: Xie

first: Peng

last: Liu

first: Lu

last: Yang

first: Bo

last: Chen

first: Cailu

last: Song

first: Hailin

last: Tang

first: Xiaoming


title: DNA methylomes of the bovine gametes and in vivo preimplantation embryos

city: Storrs

first: Xiuchun

last: Tian

state: CT

address: 1390 Storrs Road, ABL220D

department: Animal Science

institute: University of connecticut

summary: DNA methylation is an important epigenetic modification that undergoes dynamic changes in mammalian embryogenesis, during which both parental genomes are reprogrammed. Despite the many immunostaining studies that have assessed global methylation, the gene-specific DNA methylation patterns in bovine preimplantation embryos are unknown. Using reduced representation bisulfite sequencing, we determined genome-scale DNA methylation patterns of bovine sperm and individual in vivo developed oocytes and preimplantation embryos. We show that: 1) the major wave of genome-wide demethylation was completed by the 8-cell stage; 2) promoter methylation was significantly and inversely correlated with gene expression at the 8-cell and blastocyst stages; 3) sperm and oocytes have numerous differentially methylated regions (DMRs) - DMRs specific for sperm were strongly enriched in long terminal repeats (LTRs) and rapidly lost methylation in embryos, while the oocyte-specific DMRs were more frequently localized in exons and CpG islands (CGIs) and demethylated gradually across cleavage stages; 4) a unique set of DMRs were found between in vivo and in vitro matured oocytes; and 5) differential methylation between bovine gametes was confirmed in some but not all known imprinted genes. Our data provide insights into deciphering the complex epigenetic reprogramming of bovine early embryos and will serve as an important model for investigating human development and the evolutionary and regulatory roles of DNA methylation.

overall_design: Reduced representation bisulfite sequencing was used to determined genome-scale DNA methylation patterns of bovine sperm and individual in vivo developed oocytes and preimplantation embryos.

first: Z

last: Jiang

first: J

last: Lin

first: H

last: Dong

first: X

last: Zheng

first: S

last: Marjani

last: Duan

last: Ouyang


title: Adult rabbit left ventricle RNAseq

city: Salt Lake City

first: Frank

middle: B

last: Sachse

state: Utah

department: CVRTI

institute: University of Utah

summary: Adult New Zealand White rabbits (2-2.5 kg) mRNA quantification.

overall_design: High throughput RNA sequencing (Illumina HiSeq 2500, 125-cycle paired-end sequencing) was performed on adult rabbit left ventricular tissue.

first: Molly

last: Streiff

first: Azmi

last: Ahmad

first: Chris

last: Hunter


city: Ulsan

first: Hansol

last: Im

address: UNIST gil 50st

institute: Ulsan National Institute of Science and Technology

summary: We evaluated the responses of attack phase Bdellvobrio bacteriovorus HD100 when they are exposed to S. aureus biofilm.

overall_design: Experiment design of RNA seqeuncing was done as described at 'Bdellovibrio bacteriovorus HD100, a predator of Gram-negative bacteria, benefits energetically from Staphylococcus aureus biofilms without predation'

first: Robert

last: Mitchell

first: Mohammed

last: Dwidar


title: Differential Gene Expression in a Patient-Derived Xenograft from transduction of cells with shRNA targeting CDK19 and CDK8

city: Stanford

middle: Wenchen

last: Hsieh

address: 265 Campus Drive

department: Stem Cell Institute

institute: Stanford University

summary:
When CDK19 was initially discovered, it was assumed that CDK19 played a redundant role to CDK8 because they share 84% amino acid sequence similarity. However, biological clues such as CDK19s different chromosomal location and its more limited tissue distribution suggested a role distinct from CDK8
To investigate whether CDK19 and CDK8 had distinct biological functions in Triple-Negative breast cancer, we knocked down CDK19 and CDK8 in a patient-derived xenograft (PDX-C69) and examined differences in the resulting gene expression.

overall_design: EpCAM enriched PDX-C69 cells were infected with shRNA targeting CDK19, shRNA targeting CDK8, 'empty vector' control shRNA and grown in organoid culture conditions for 72 hours

middle: W

first: Michael

last: Clarke


title: Bone marrow stromal cell antigen 2 is a novel therapeutic target of glioblastoma stem cells

city: Seoul

first: Eun Hee

last: Yi

state: Seoul

address: 103 Daehangno, Jongno-gu

department: Pharmacology

institute: Seoul National University College of Medicine

summary: we identified BST-2 is a novel therapeutic target and BST-2 depletion leads to downregulated CSC-related signaling molecules.

overall_design: To understand the BST-2 functions on cancer stem cell biology in GBM, we established BST-2 stable knock down GBM primary cells and analyzed by using microarray.

first: Eun-Hee

first: Sang-Kyu

last: Ye


title: MiRNA expression data of FPCK-1-1 human colonic adenoma cells and its-derivative FPCKpP1-4 adenocarcinoma cells

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: Analysis of FPCK-1-1 human colonic adenoma cells and FPCKpP1-4 adenocarcinoma cells derived from FPCK-1-1 cells by chronic inflammation. Several miRNAs are aberrantly expressed in FPCKpP1-4 cells. Results provide insight into the molecular basis of chronic inflammation-related colon carcinogenesis.

overall_design: MiRNA expression profiles of FPCK-1-1 cell line and its-derivative FPCKpP1-4 cell line were analyzed. Two samples.

first: Yusuke

last: Kanda

first: Tokuichi

last: Kawaguchi

first: Mitsuhiko

last: Osaki

first: Kunishige

last: Onuma

first: Takahiro

last: Ochiya

first: Tomoyuki

last: Kitagawa

first: Futoshi

last: Okada


title: The stem cell gene ABCB5 mediates cancer resistance to apoptosis

city: Boston

first: Natasha

middle: Y

last: Frank

state: MA

address: 320 Longwood Avenue

department: Medicine

institute: Children's Hospital Boston

summary: Cancer stem cells (CSC) responsible for disease progression and therapeutic resistance have been identified in several human malignancies, including colorectal cancer (CRC). However, the molecular mechanisms through which CSC drive tumor growth are incompletely understood. ABCB5, a member of the ATP-binding cassette superfamily of active transporters, serves as a CSC-specific multidrug resistance mechanism in diverse human malignancies. Additionally, ABCB5 has recently been demonstrated to function as an anti-apoptotic gene in tissue-specific non-malignant stem cells. Here we demonstrate that ABCB5 also serves an anti-apoptotic role required for CSC maintenance in human cancer. Targeted inhibition of ABCB5, previously shown to be preferentially expressed on CD133-positive CRC stem cells, induced tumor cell apoptosis in vitro and in vivo and inhibited human CRC growth in NSG recipient mice. Mechanistically, ABCB5-positive tumor cell ablation through monoclonal antibody-mediated blockade or shRNA-mediated gene knockdown resulted in diminished production of the receptor tyrosine kinase AXL, a pro-tumorigenic molecule identified herein to be preferentially produced by CRC stem cells. Restoration of AXL expression through gene transfection in ABCB5 knockdown tumors partially restored tumor growth, demonstrating that ABCB5-positive CRC stem cells drive tumorigenicity at least in part through production of AXL. Our results establish a novel anti-apoptotic function of ABCB5 in human cancer and indicate that targeted blockade of ABCB5 represents a novel strategy for CSC eradication, independent of its previously established function as a multidrug resistance mediator.

overall_design: ABCB5-positive cells and ABCB5-negative cell populations were isolated by FACS cell sorting using anti-ABCB5 mAb as described (Ksander et al., Nature, 2014). Microarray analyses were performed on purified ABCB5+ (n=4) and ABCB5- (n=4) cell subsets derived from the established colon cancer cell lines COLO741, SW480, HT29 and HCT116. Total RNA isolated from sorted cell populations was processed and hybridized onto Human Gene 1.0 ST Array (Affymetrix) .

first: Qin

last: Guo


title: microRNA expression profiling in HPV-16/HIV associated Cervical Cancer

city: trivandrum

first: Radhakrishna

middle: Madhavan

last: Pillai

state: KERALA

address: poojappura

department: Cancer Research Program

institute: Rajiv Gandhi Centre for Biotechnology

summary:
Identifying the differentially expressed miRNAs in Cervical cancer patients infected with only one virus i.e. either HIV or HPV-16 and patients infected with both viruses HIV and HPV-16 with respect to their controls which is the healthy population not infected by either HIV or any HPV
The miRNA array was performed using the affymetrix GeneChip® miRNA 3.0 Array (Affymetrix, Santa Clara, California, United States). The chip was processed using a commercial Affymetrix array service (GeneTech Biotechnology Limited Company, Shanghai, China). The affymetrix GeneChip® miRNA 3.0 Array contains 2,999 probe sets unique to human, mouse and rat pre-miRNA hairpin sequences, 2,216 human snoRNA and scaRNA probe sets and covers 153 organisms (19,724 probe sets). Raw data sets were extracted from all Cel files (raw intensity file) after scanning of slides. These raw data sets were separately analyzed using Expression Console and GeneSpring GX12.5 software followed by differential miRNA expression, fold change & cluster analysis.

overall_design: We selected 3 samples each from the following categories (HIV+& HPV16+ ; HIV+only ; HPV-16+only and healthy population control which are not infected with either HPV or HIV) for the microRNA array. The HPV status of these samples was confirmed using HPV type-specific E7 PCR bead-based multiplex genotyping (TS-MPG).We isolated the total RNA from these 12 samples and performed the miRNA array (Affymetrix platform) to identify the  differentially expressed miRNAs in cervical cancer patients infected with only one virus i.e. either HIV or HPV-16 and patients infected with both viruses HIV and HPV-16 with respect to their controls (healthy population).

first: Janki

middle: M

last: Vijayamma

first: Aswathy

last: Paul

first: Smita

last: Joshi

first: G

last: Reshmi

first: Tarik

last: Gheit

first: M

last: Tommasino

first: Jissa

last: Vinoda

first: R

last: Sankaranarayanan


title: Adaptative response of Debaryomyces hansenii in co-culture with Yarrowia lipolytica

city: Thiverval Grignon

first: Reine

last: Malek

address: Avenue Lucien Brétignières

institute: INRA, UMR 1319 MICALIS

summary:
A comparison between the coculture of Debaryomyces hansenii with Yarrowia lipolytica and the monoculture of Debaryomyces hansenii, was carried out at two hours of culture (12h and 27h), in order to understand the metabolic changes induced in D. hansenii when grown in coculture with Y. lipolytica .
The transcriptomic study was carried out using Agilent 8X15k slides with a custom oligoset designed by V. Loux using the Debaryomyces hansenii ORFeome extracted from genolevures database

overall_design: Two conditions experiment, coculture of D. hansenii versus monoculture of D. hansenii at 12h and 27h of culture. Dye switches were done using four biological replicates for both monoculture and coculture of D. hansenii at 12 h and 27h.

first: Pascal

last: Bonnarme

first: Françoise

last: Irlinger

first: Pascale

last: Frey-Klett

first: Djamila

last: Onésime

first: Julie

last: Aubert

first: Valentin

last: Loux

first: Jean-Marie

last: Beckerich


title: Expression data from OVA-induced allergic mice [Agilent]

city: Beijing

first: LI

middle: Yong

last: Ning

address: 7 Panjiayuan Nanli

institute: China National Center for Food Safety Risk Assessment

summary:
IgE antibodies are key mediators of food allergy, and the production of IgE is tightly regulated at the moleculaer and cellular level in the germinal center of lymph glands where specific sets of genes are up-regulated.
We used microarrays to detail the global programme of gene expression underlying ovalbumin-induced allergy and identified distinct classes of  up-regulated genes during this process.

overall_design: Spleens of control and  OVA-induced allergic mice  were harvested for RNA extraction and hybridization on Agilent microarrays.

first: Nanan

last: Sun

first: Hui

last: Yang


title: Long non-coding RNA Expression Profiling in Hepatocellular Carcinoma (HCC) and in normal liver

status: Public on Jul 31 2018

city: Heidelberg

first: Sven

last: Diederichs

address: Im Neuenheimer Feld 280

department: RNA Biology & Cancer

country: Germany

institute: German Cancer Research Center (DKFZ)

summary: The expression of long non-coding RNAs - lncRNAs - was profiled in the liver cancer Hepatocellular Carcinoma - HCC - and in normal liver tissues using the Invitrogen NCode Human lncRNA Array Platform.

overall_design: 32 tumor samples, 7 normal samples, data provided as log2 signal intensities quantile normalized with a minimum signal intensity (threshold 1.0)

first: Maria

last: Polycarpou-Schwarz

first: Marcel

last: Klingenberg

first: Thomas

last: Longerich

first: Peter

last: Schirmacher


title: The polycomb protein MEL-18/PCGF2 regulates ErbB phosphorylation in HER2-positive breast cancer

first: Hyeong-Seok

last: Joo

address: Wangsimni-ro

department: Institute of Personalized Medicine

institute: Hanyang University

summary: Gene expression analysis on MEL-18-knockdown BT474 cells. MEL-18, a polycomb group protein and a member of the polycomb repressive complex 1 (PRC1), have suggested as a tumor suppressor in several cancer, including breast cancer. The results provides that the depletion of MEL-18 in HER2-positive breast cancer causes the activation of ErbB signaling pathway. We proposed that MEL-18 is a novel prognostic and therapeutic marker for HER2-positive breast cancer.

overall_design: Total RNA was isolated from the cells using Trizol reagent. BT474 cells stably infected with lentiviruses encoding MEL-18 shRNA (shMEL) compared to its control (shCon)

first: Hee-Joo

last: Choi

first: Taekwon

last: Son

first: Hyung-Yong

last: Kim

first: Jeong-Yeon

last: Lee

first: Gu

last: Kong


title: Genome-wide comparison of differentially expressed genes in hepatoma cell lines with and without treatment of dimethyl dicarboxylate biphenyl

city: Seongnam

first: Young Min

last: Park

state: Gyeonggi

address: 20, Seohyeon Road 180th street, Bundang-gu

department: Biomedical Research Center

institute: Bundang Jesaeng General Hospital

summary: Backgrounds/Aims: Dimethyl dicarboxylate biphenyl (DDB), a synthetic compound of Schizandrin C, is an adjuvant medicine to support the treatment of various hepatitis. Although it protects hepatocytes from different toxic chemicals, the principal pharmaco-biological mechanism of DDB is still unclear. This study aimed to identify genes changed by the DDB in hepatoma cell lines. Methods: Using Agilent SurePrint G3 Human GE 8X60K, V3 Microarrays, we analyzed the DDB-induced genes genome-widely in a hepatoblastoma (HB) cell line, HepG2, and two hepatocellular carcinomas (HCC), Hep3Band Huh7, after 48 hours of exposure to 0.1 mM DDB. We explored data using the software packages edgeR and limma and KEGG pathway analysis and re-confirmed with RT-PCR for several selected genes. Results: Hierarchical clustering, heatmap, and MDS plot analysis showed that HepG2 belonged to the different cluster from the HCC cell lines. When compared among the DDB-untreated control cells (con), number of genes expressed higher and lower (≥1.5 folds (≥.2 folds)) than the other was 5530 vs. 5250 (2916 vs. 2890) in the Hep3Bcon vs. HepG2con, 5931 vs. 5411 (3172 vs. 3197) in the Huh7con vs. HepG2con, and 4835 vs. 4962 (2483 vs. 2497) in the Huh7con vs. Hep3Bcon, respectively. In the comparison of the DDB-untreated and treated cells in each cell line, the up- and downregulated genes (≥1.5 folds (≥.2 folds)) were 328 vs. 696 (53 vs. 76) in HepG2, 226 vs. 250 (45 vs. 44) in Hep3B, and 250 vs. 229 (51 vs. 47) in Huh7, respectively. Only the CYP1A1 upregulation was significantly common to all three cells. Curiously, the metallothionein genes (MT1G, MT1L, MT2A, MT1E, MT1B, MT1HL1, MT1F, and MT1A) tended to be upregulated by DDB. We also noticed tenascin as a target gene regulating the attachment of cells to the extracellular matrix. Conclusions: HB and HCC have different properties regarding the gene expression in the baseline state. The different responses of each cell line to the DDB are inherent given the genomewide difference of gene expression. CYP1A1 and metallothionein are the target genes of DDB that are common to the three cell lines.

overall_design: Dimethyl dicarboxylate biphenyl (DDB)-induced gene expression in three different human hepatoma cell lines, including HepG2, Hep3B, and Huh7, was compared after 48 h of culture with 0.1 mmol/L DDB between the DDB-treated and -untreated cell. Also, we compared gene expression between Control-HepG2 and Control-Hep3B, between Control-HepG2 and Control-Huh7, and between Control-Hep3B and Control-Huh7. DDB DMSO (7.6 g/L) was used as a control reagent.

first: Young

first: Su

middle: H

last: Jung


title: A comparison of the intestinal phenotype and transcriptome profile analysis in the oral-fed mice with substances to affect the intestinal homeostasis

first: Se-Na

address: SNU Research Park, 1 Gwanak-gu

institute: International Vaccine Institute

summary: Epithelial cells in the intestinal mucosa maintain gut homeostasis by interacting with different types of microbiota. Proper appropriate immune responses in the intestinal epithelium are essential for the preservation of the intestinal homeostasis. In the present study, we aimed to identify genotypic and phenotypic changes in mice following oral feeding of various substances which has been shown to differentially affect intestinal homeostasis. We orally fed C57BL/6 mice for either one or seven days with one of the four substances: dextran sulfate sodium (DSS); Typhoid VI Polysaccharide vaccine (Vi vaccine); antibiotic cocktails (AB) of ampicillin, vancomycin, neomycin, and metronidazole; or(probiotics)consisting of Lactobacillus Rhamnosus R0011and L. Acidophilus R0052.While DSS and AB feeding resulted in severe gut pathology characterized by infiltration of inflammatory cells, epithelium shedding, and distortion of paneth cells. Vi vaccine and probiotics feeding resulted in phenotypic improvement of the gut health characterized by epithelial cell proliferation and increased formation of tight junctions between epithelial cells. Interestingly, microarray data showed significant increase in the expression levels of genes regulating cell proliferation and intestinal homeostasis in the gut epithelium of probiotics-and Vi vaccine-fed mice compared to DSS-or AB-fed mice. In addition, expression levels of genes regulating cell death and inflammation were significantly increased in the gut epithelium of DSS- and AB-fed mice. These results suggest that intestinal homeostasis play a pivotal role in maintaining gut health and, subsequently, in protecting host against enteric bacteria and external pathogens infection.

overall_design: The design of our study was focused on clarify genotypic and phenotypic changes in mice following oral feeding of various substances which has been shown to differentially affect intestinal homeostasis. Mice were randomly divided into 5 groups according to body weight (n =10 for each group); WT (distilled water), DSS (only 4% DSS in the drinking water), Vi vaccine (Oral feeding with 0.006mg/ 200ul of Vi vaccine diluted in phosphate-buffered saline (PBS)), AB (only AB cocktails in the drinking water) and Probiotics mixture (oral feeding with live 2 × 109 CFU in 200ul PBS).The mice were oral fed with one of the four materials for one day or seven days and then switched to drinking water for 1 day.

first: Young-Joo

first: Eun-Ji

first: Jung-A

first: Hye-Ran

last: Cha

first: Man-Ki

last: Song

first: Oran

last: Kweon


title: Expression data from mouse CD19-targeted CAR (chimeric antigen receptor) T cells after antigen stimulation [expression array]

city: Tampa

first: Gongbo

last: Li

state: Florida

address: 3011 W Holly Dr. MRC 2068

institute: Moffitt Cancer Center

summary:
Second-generation CD19-targeted chimeric antigen receptors (CAR) have an antigen-binding domain fused to transmembrane, co-stimulatory, and CD3ζ domains. The two CARs with regulatory approval include a CD28 or 4-1BB co-stimulatory domain. While both CARs achieve similar clinical outcomes, biologic differences between the two endodomains have become apparent but not completely understood.
The objective is to evaluate gene expression in different mouse CD19-targeted CAR T cells, including m19z, m1928z and m19-musBBz.

overall_design: Different CAR T cells were stimulated with antigen presenting cells overnight for RNA extraction and hybridization on Affymetrix microarrays. Nine samples were analyzed.

first: Marco

last: Davila


title: The transcriptional network of wild type ERG and ERG mutant at K362

city: Biella

first: giovanna

last: chiorino

address: via malta 3

department: Cancer Genomics

institute: Fondo Edo Tempia

summary: We have identified a specific site in the ERG protein that undergoes post-transcriptional modification. We have mutated this site and generated stably expressing LNCaP cell lines. In this study we evaluated the transcriptional profile induced by ERG in LNCaP stably expressing ERG wild type , ERG mutant or empty vector (EV).

overall_design: Two replicates for each condition are considered (2 control cell lines, two cell lines with wild type ERG overexpression and two cell lines with mutant ERG overexpression).

first: Giuseppina

last: Carbone

first: Giovanna

last: Chiorino

first: Caro

last: Catapano


title: miRNA expression data from cultivated Human Thymic Epithelial Cells (hTECs) in comparison with cultivated Human Epidermal derived Keratinocytes (hEKs)

city: Lausanne

first: Melissa

last: Maggioni

address: Station 15

department: IBI

country: Switzerland

institute: EPFL

summary:
The thymic epithelium and the epidermis display many common features despite their different structure, function and embryonic origin.
We used microarrays to uncover differences and similarities in the miRNA expression profile of hTECs and hEKs and investigate their significance for the peculiar organization of the thymic structure.

overall_design: miRNA expression was measured in cultivated  hEKs, EpCAM negative hTECs and in EpCAM positive hTECs. Three indipendent experiment were performed to collected samples

first: Matteo

last: Pluchinotta

first: Yann

last: Barrandon


title: Expression data of renal cancer cell treated with Oncolytic virus VSVd51 and Fumaric acid esters such as Dimethyl fumarate

status: Public on Jul 30 2018

city: Ottawa

first: Mohammed

last: Selman

state: ON

address: 501 Smyth Road

department: Cancer Center

institute: Ottawa Hospital

summary:
We propose a strategy to boost the therapeutic efficacy of Oncolytic therapy by combining it with  fumaric acid ester such as Dimethyl fumarate (DMF)
The mechanism of action was examined by microarray analysis using the Affymetrix Human PrimeView Array.

overall_design: 786-0 cells were plated in 6-well dishes and allowed to adhere overnight. The next day, cells were pretreated for 4hours with DMF, DEF, DEM and DMM or the vehicle. Following pre-treatment, the cells were infected with VSVΔ51 at an MOI of 0.01 or left uninfected. Twenty-four hours post infection, RNA was collected using an RNA-easy kit . Biological triplicates were subsequently pooled and RNA quality was measured using Agilent 2100 Bioanalyzer (Agilent Technologies) before hybridization. Hybridized to Affymetrix Human PrimeView Array . Microarray data was processed using Transcriptome Analysis Console (TAC) 3.0 under default parameters of Gene Level Differential Expression Analysis. Fold change in gene expression was calculated for each gene in relation to uninfected, untreated control.

first: Jean-Simon

last: Diallo


title: Expression data from rats liver

city: Chongqing

first: XINYU

last: LI

address: 1 YOUYI ROAD

institute: The First Affiliated Hospital of Chongqing Medical University

summary:
Diabetes exerts adverse effects on the initiation or progression of diabetes and metabolic syndrome of in the next generation. In past studies, limited attention has been given to the fathers’ role in shaping the metabolic landscape of offspring.
We used microarrays to detail the global programme of gene expression identified differientially expressed genes during this process.

overall_design: Our study was designed to investigate how paternal hyperglycemia exerts an intergenerational effect in mammals as well as the underlying mechanisms.Hyperglycemia was introduced in male rats by intraperitoneally injected streptozotocin and these males were bred with healthy female rats to generate offspring. The metabolic profiles of the progeny were assessed, and gene expression profiles related to lipid metabolism were investigated.

first: Xiaoqiu

last: Xiao

first: Xinyu


title: Whole-blood transcriptional signatures composed of erythropoietic and Nrf2-regulated genes differ between cerebral malaria and severe malarial anemia

status: Public on Jul 28 2018

city: Ann Arbor

first: Simpa

middle: S

last: Salami

state: MI

address: 1500 E Medical Center Dr

department: Urology

institute: University of Michigan

summary: We compared genome-wide transcription profiles of whole blood obtained from Ugandan children with acute CM (n=17) or SMA (n=17) and community children without Plasmodium falciparum infection (n=12) and determined the relationships between gene expression, hematological indices, and relevant plasma biomarkers. Results demonstrated both CM and SMA predominantly upregulated enrichment of dendritic cell (DC), inflammatory/TLR/chemokines, monocyte, and antigen presentation modules but downregulated enrichment of lymphocyte modules. Neurodegenerative disease pathways showed modest upregulation during CM. Nrf2-regulated genes were over-expressed in children with SMA compared to CM, especially those with HbSS, corresponding with increased plasma heme oxygenase-1. Reticulocyte-specific gene expression was markedly decreased in CM relative to SMA despite higher hemoglobin levels and appropriate increases in erythropoietin. Viral sensing/IRF2 module expression and plasma IP-10/CXCL10 negatively correlated with reticulocyte-specific signatures. This study concludes that, compared to SMA, CM is associated with downregulation of Nrf2-related and reticulocyte-specific signatures by whole-blood transcriptomics. Future studies are needed to confirm these findings and assess pathways that may be amenable to interventions to ameliorate CM and SMA.

overall_design: Total RNA was purified from whole blood and depleted of globin mRNA prior to amplification and processing for gene expression profiling using Illumina HumanHT-12 v4 Expression BeadChip. Samples were processed in three Batches using random sampling and differential expression was performed between the groups (CM, SMA, CC) adjusting for Sickle cell disease status, HRP2 levels, and Batch effects for the following comparisons: CM vs CC; SMA vs CC; CM vs SMA relative to CC.

first: Srinivas

last: Nallandhighal

first: Gregory

last: Park

first: Yen-Yi

last: Ho

first: Robert

middle: O

last: Opoka

first: Chandy

last: John

first: Tuan

last: Tran


title: mRNA of fed and starved C. elegans L1 larvae 3 generations following control, short-term dauer or long-term dauer conditions

status: Public on Jul 27 2018

city: Eugene

first: Amy

middle: K

last: Webster

state: Oregon

address: Institute of Ecology and Evolution

institute: University of Oregon

summary: N2 worms were subjected to control (well-fed), short-term dauer (6 d), or long-term dauer (40 - 49 d) conditions. Worms were recovered and maintained well-fed for 3 generations. F3 progeny were collected as fed or starved L1 larvae.

overall_design: 6 conditions include: control fed, control starved, short-term dauer fed, short-term dauer starved, long-term dauer fed, and long-term dauer starve. 3-12 biological replicates were sequenced per condition

first: A

first: R

last: Chitrakar

first: L

last: Baugh


title: Hepatic Gene Expression during the Perinatal Transition in the Rat

city: Providence

first: Jennifer

middle: Ann

last: Sanders

state: RI

address: 593 Eddy Street

department: Pediatric Endocrinology

institute: Rhode Island Hospital

summary: During the immediate postnatal period, the liver, with its role in energy metabolism and macromolecule synthesis, plays a central role in the perinatal transition. Using RNA microarrays and several complementary computational analyses, we characterized changes in hepatic gene expression in the rat across a developmental period starting with the late gestation fetus (embryonic day 21), and including 30 min postnatal (PN), 4 hr PN, 12 hr PN, 1 day PN and 1 week after birth. Following subtle changes in gene expression at the earliest postnatal time point, there were marked changes that occurred between 4 hr and 12 hr after birth. These reflected changes in multiple metabolic pathways, with expression of enzymes involved in glycolysis and cholesterol synthesis showing the greatest change. Over 50% of nuclear-encoded mitochondrial genes changed in the first 7 days of postnatal life, with 25% changing within the first 24 hr. We also observed changes coinciding with a transient period of synchronous hepatocyte proliferation that we had observed previously, which occurs during the first postnatal week. Analysis for upstream regulators of gene expression indicated multiple initiating factors, including cell stress, hormones and cytokines. Also implicated were multiple canonical transcription factor networks. We conclude that changes in gene expression during the early phases of the perinatal transition involve a complex, choreographed network of signaling pathways that respond to a variety of environmental stimuli. This transcriptomic response during the immediate postnatal period reflects a complex metabolic adaptive response that incorporates a panoply of signaling pathways and transcriptional regulators.

overall_design: Term (E21) and early postnatal (30 min, 4hr, 12hr, 1day and 7 day after birth) liver was harvested from triplicate dams.  RNA was isolated using the Rneasy kit.  Affymetrix Rat transcriptome 1.0 arrays were used.

first: Edward

last: Hurley

first: Valerie

last: Zabala

first: Joan

last: Boylan

first: Philip

last: Gruppuso


title: Foxc1 and Foxc2 are necessary to maintain glomerular podocytes

status: Public on Jul 25 2018

city: Isehara

first: Masaru

last: Motojima

address: 143 Shimokasuya

department: Clinical Pharmacology

institute: Tokai University School of Medicine

summary:
Foxc1 and Foxc2 are highly expressed in adult podocytes. To bypass embryonic lethality of Foxc1 and Foxc2 KO, mice ubiquitously expressing inducible-Cre (ROSA26-CreERT2) were mated with floxed-Foxc1 and floxed-Foxc2 mice.
We used microarrays to detail effects of deletions of Foxc1 and Foxc2 on podocyte gene expression profiles in adult podocyte in vivo and in vitro.

overall_design: The CreERT2 was activated in adult mice by administrations of tamoxifen. Isolated glomeruli were subjected to total RNA preparation. Altanatively, primaly cultured podocytes were treated with the active form of tamoxifen and total RNA was prepared on 4 or 7 days after the treatment.


title: RNAi-mediated MLL/AF4 knock-down time course

status: Public on Jul 21 2018

city: Rotterdam

first: Patricia

last: Garrido Castro

address: Wytemaweg 80

department: Dept. Pediatrics

institute: Erasmus MC - Sophia Children's Hospital

summary: MLL/AF4 fusion transcript knock-down time course in the MLL/AF4-positive B-cell precursor ALL cell line SEM using MLL/AF4 fusion site-specific siRNAs (siMLL/AF4). The aim was to identify genes responsive to MLL/AF4 expression modulation.

overall_design: The B-cell precursor ALL cell line SEM cell line was sequentially transfected with either siRNAs against MLL/AF4 (siMLL/AF4), or control siRNA (siCtrl) at two day intervals for up to 3 times, representing a siRNA treatment time course of 6 days. For internal QC, mock-electroporated (MOCK) samples, representing pulse controls,  were also included at the first and second electroporation. Material was harvested for analyses immediately prior to the subsequent electroporation and at the final time point, two days after the 3rd electroporation, corresponding to a sustained MLL/AF4 knock-down period of 2 (TP1), 4 (TP2) and 6 days (TP3), respectively. Differential expression analysis were performed for  siCtrl and siMLL/AF4 samples at TP1, TP2 and TP3.

first: Olaf

last: Heidenreich


title: Transcriptome-wide gene expression analysis of the cancer cell lines after treatiment with telomerase inhibitor Imetelstat (GRN163L)

status: Public on Jul 19 2018

city: Birmingham

first: Narendra

last: Wajapeyee

state: AL

address: 720 20th Street South, Kaul 540A

department: Department of Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

summary: GRN163L is a potent and specific telomerase inhibitor and in clinical trials for cancer treatment. To identify the biomarker that might predict response to telomease based therapy,  gene expression analysis of the cancer cell lines after treatiment with telomerase inhibitor Imetelstat (GRN163L) was performed.

overall_design: HCT116, Colo205, OVCAR5 cells were either vehicle treated or Imetelstat treated for 2 weeks and then total RNA was preppared, which was then used to analyze for gene expression using Illumina expression array.

first: Romi

last: Gupta

first: Shaillay

last: Dogra


title: Normal and Cancer Exosomes Induced Gene Expression Profiles in Primary Human Normal Oral Keratinocytes

status: Public on Jul 16 2018

city: London

first: Muy-Teck

last: Teh

state: England

address: Blizard Building, 4, Newark Street,

department: Centre for Clinical & Diagnostic Oral Sciences

institute: Queen Mary University of London

summary: Gene expression reprogramming in normal oral keratinocytes following exposure to normal or cancer-derived exosomes.

overall_design: Gene profiling of normal human primary oral keratinocytes (OK113) exposed to exosomes derived from either normal (OK113, NK4, NOK368) (n=3) or head and neck squamous cell carcinoma cell lines (CA1, CALH2, SqCC/Y1, SVpgC2A, SVFN10) (n=5).

first: Muy

middle: T

first: Fatima

last: Qadir


title: Genome-wide analysis of gene expression of cutaneous lupus and cutaneous psoriasis lesions

status: Public on Jul 15 2018

city: Worcester

first: John

last: Harris

address: 364 Plantation St

department: Dermatology

institute: University of Massachusetts Medical School

summary: Human skin samples from cutaneous lupus subtypes, psoriasis, and normal patients were used to corroborate findings of Fas Ligand elevation in a murine model of cutaneous lupus

overall_design: 56 deidentified human samples from formalin fixed, paraffin-embedded skin; 6 chronic cutaneous lupus, 12 subacute cutaneous lupus, 7 acute cutaneous lupus, 14 control skin, and 17 psoriasis

first: Wei-Che

middle: C

last: Ko


title: Expression data of exosomal miRNAs extracted from plasma [Affymetrix miRNA 4.0]

status: Public on Jul 03 2018

city: Chengdu

first: Bai

last: Hao

state: Sichuan

address: Wuhou District Guoxue Lane 37

department: Laboratory Medicine

institute: West China Hospital of Sichuan University

summary:
Tuberculosis (TB) is difficult to diagnose under complex clinical conditions. Exosomal miRNAs have emerged as promising disease biomarkers. We aim to investigate the potential of exosomal miRNAs to assist with TB clinical diagnosis.
In the present research, we used the Affymetrix Genechip miRNA 4.0 Array to investgate the profiles of differentially expressed miRNAs (DEMs) in the exosomes of peripheral blood plasma. As a result, exosomal miRNA profiling yielded a total of 102 DEMs (98 with up-expression and 4 with down-expression) between the TB (pulmonary tuberculosis and tuberculosis meningitis) patients and controls.

overall_design: Peripheral blood samples of 11 TB patients and 8 healthy individuals were collected for the for exosomal miRNAs extraction and hybridization on Affymetrix microarrays. In TB group, the most frequent (PTB) and the most lethal (TBM) forms were selected: PTB-1, PTB-2, PTB-3, PTB-4, PTB-5, PTB-6, PTB-7, TBM-1, TBM-2, TBM-3 and TBM-4. Meanwhile, 8 healthy individuals were selected as controls: HC-1, HC-2, HC-3, HC-4, HC-5, HC-6, HC-7 and HC-8.

first: Xuejiao

last: Hu

first: Shun

last: Liao

first: Hao

last: Bai

first: Lijuan

last: Wu

first: Minjin

last: Wang

first: Qian

first: Juan

last: Zhou

first: Lin

last: Jiao

first: Xuerong

last: Chen

first: Yanhong

first: Xiaojun

last: Lu

first: Binwu

last: Ying

first: Zhaolei

last: Zhang

first: Weimin

last: Li


title: Comparative Transcriptomics of Limb Regeneration in Ambystoma salamanders

status: Public on Jul 10 2018

city: Lexington

first: Varun

middle: Bhamidipati

last: Dwaraka

state: Kentucky

address: 741 South Limestone St.

department: Spinal Cord and Brain Injury Research Center

institute: University of Kentucky

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

sample_organism:
Ambystoma mexicanum
Ambystoma maculatum
Ambystoma andersoni

overall_design: Refer to individual Series


title: Comparative Transcriptomics of Limb Regeneration: Identification of Conserved Expression Changes Among Three Species of Ambystoma [microarray]

status: Public on Jul 04 2018

summary: Transcriptome studies are revealing the complex gene expression basis of limb regeneration in the primary salamander model – Ambystoma mexicanum (axolotl). To better understand this complexity, there is need to extend analyses to additional salamander species. Using microarray and RNA-Seq, we performed a comparative transcriptomic study using A. mexicanum and two other ambystomatid salamanders: A. andersoni, and A. maculatum. Salamanders were administered forelimb amputations and RNA was isolated and analyzed to identify 405 non-redundant genes that were commonly, differentially expressed 24 hours post amputation. Many of the upregulated genes are predicted to function in wound healing and developmental processes, while many of the downregulated genes are typically expressed in muscle. The conserved transcriptional changes identified in this study provide a high-confidence dataset for identifying factors that simultaneous orchestrate wound healing and regeneration processes in response to injury, and more generally for identifying genes that are essential for salamander limb regeneration.

overall_design: Ambystoma mexicanum forelimbs were amputated mid-zeugopod. 1.0mm samples of heterogeneous tissue from regenerating Ambystoma mexicanum limb tip were removed and used for RNA extraction. Three replicates samples were collected for each time point, with each replicate formed by pooling tissue from 5 different larvae.

first: Jeramiah

middle: J

last: Smith

first: M

middle: R

last: Woodcock

first: S

last: Voss


title: Generating mesenchymal stem cells in 3D from human embryonic stem cell spheroids

city: Macao

first: Renhe

last: Xu

address: Avenida de Universidade  Taipa

department: Faculty of Health Sciences

institute: University of Macao

summary: Background: Mesenchymal stem cells (MSC) derived from human embryonic stem cells (hESC), named EMSC here, have been found efficacious in animal models of autoimmune, inflammatory, and degenerative diseases. However, all the EMSC derivation methods reported so far are in two-dimensional (2D) culture systems, which are of low efficiency and high cost, difficult for large-scale production for research and therapeutic applications.   Methods: We established a 3D system that allowed differentiation of hESC spheroids into MSC spheroids (EMSCSp) following treatment with BMP4 and A8301 for 5 days and subsequent culture in a MSC medium for about 15 days. All the procedures were conducted in one vessel without intermediate passaging.  Results: EMSCsp cells were efficiently derived from hESC spheroids within 20 days in the 3D culture system, which could be scaled up from a small culture vessel to a 100-ml plastic bag. EMSCSp could further differentiate into spheroids of chondrocytes or adipocytes. EMSCSp could also reattach and form a 2D-monolayer culture (EMSCSp-ML). Compared to EMSC differentiated in monolayer, EMSCSp-ML had faster proliferation and higher yield, and developed less apoptosis and slower senescence. EMSCSp-ML also retained immune-modulatory effects in vitro and therapeutic effects on two mouse models of colitis.   Conclusions: The 3D method provides a simple and economic system for large-scale production of EMSC as an unlimited source of the therapeutically promising cells.

overall_design: In this study, we show that hESC cultured as spheroids (hESCSp) could differentiate into EMSC spheroids (EMSCSp) also via an intermediate trophoblast step. Unlike the 2D differentiation systems, our new method allows all the multi-step differentiation procedures to be completed in one vessel in 3D without any need for cell passaging. EMSCSp could further differentiate into spheroids of chondrocytes and adipocytes or reattached and passaged in monolayer (EMSCSp-ML) without compromising their multipotency. Compared to EMSC differentiated in monolayer (EMSCML) as we reported before [9], EMSCSp-ML had faster proliferation and higher yield, and developed less apoptosis and slower senescence. EMSCSp-ML also retained immune-modulatory effects in vitro and therapeutic effects on a mouse colitis model. Thus, the 3D method is advantageous over the 2D methods for large-scale production of EMSCs for potential clinic application.

first: Bin

last: Jiang

first: Li

last: Yan

first: Enqin

first: Xiaoyan

first: Dejin

last: Zheng

first: Jung

last: Park

first: Xin

first: Wing

last: Cheung

last: Du

first: Gregory

last: Cheng

first: Ren-He


title: Transcriptional profiling of gene expression changes in immune cells of human subjects treated with Varilumab

status: Public on Jun 30 2018

city: Hampton

first: Venky

last: Ramakrishna

state: NJ

address: 53 Frontage Rd, Suite 220

department: R&D Human Immunology

institute: Celldex Therapeutics

summary: This study evaluatated transcriptomic changes in RNA isolated from whole-blood samples from 12 patients receiving different doses of Varlilumab at several different time points following treatment.  The aim of this study was to determine the extent to which expression of inflammatory molecules changes over time in response to treatment with Varilumab, a fully human monoclonal antibody (mAb) that targets CD27.

overall_design: Total RNA from whole-blood samples was isolated before treatment with Varilumab and 1, 7, and 28 days after treatment. The data set comprises 48 samples taken from 12 human subjects at 4 time points: Study Day (SD) 1, which is pre-treatment, SD2, SD8, and SD29.  5 doses of Varilumab were used--0.1 mg, 0.3 mg, 1 mg, 3 mg, and 10 mg. Two subjects received 0.1 mg, 2 subjects 0.3 mg, 3 subjects 1mg, 3 subjects 3mg, and 2 subjects 10 mg.

last: Ramakrisha


title: Expression data from retina and reinoblastoma tumour samples

city: Chennai

first: Sailaja

middle: V

last: Elchuri

state: Tamil Nadu

address: No18, College Road, Nungambakkam

department: Nanobiotechnology

institute: Vision Research Foundation

summary:
Retinoblastoma (Rb) progresses from retina to noninvasive Rb and then into invasive Rb. Global gene expression changes leading to these changes were investigated presently in Rb subtypes. The pathological staging of the tumours is compared to global gene expression profiles.
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process.

overall_design: Retina and Rb subtypes tissues were obtained from donor eyeballs and informed concent respectively.   RNA extraction extraction and hybridization on Affymetrix microarrays were performed to under stand tumour progression with an intent to identify candidate biomarkers for Rb diagnosis and therapy.

first: Ravikanth

last: Danda

first: Srujana

last: Chittipothi

first: Krishna

last: Kumar

first: Debashis

last: Sahoo


title: Comparative Transcriptomics of Limb Regeneration: Identification of Conserved Expression Changes Among Three Species of Ambystoma [RNA-Seq]

first: Varun

last: Dwaraka

platform_organism:
Ambystoma mexicanum
Ambystoma maculatum
Ambystoma andersoni

overall_design: Forelimbs were amputated mid-zeugopod in all animals. 1.0mm samples of heterogeneous tissue from regenerating limb tips were removed and used for RNA extraction. Three replicates samples were collected for each time point, with each replicate formed by pooling tissue from 5 different larvae.

middle: B

first: Melvin

last: Woodcock

first: Jeramiah

last: Smith

first: Stephen


title: IDENTIFICATION OF A NOVEL GENETIC PROGRAM AT THE INITIATION OF COLON CANCER DEVELOPMENT.

city: Lyon

first: Anne

last: Wierinckx

state: select a state

address: 8, av Rockefeller

institute: University Lyon1

summary: As a result of a chronic inflammation or in response to the constitutive activation of the beta-catenin pathway, the generation of reactive oxygen species causes telomere attrition and triggers intestinal cell commitment into a senescence program. Nonetheless, such events are known to promote their neoplastic transformation, suggesting that the escape from oxidative stress-induced senescence favors the emergence of deleterious cells. By setting up an in vitro model, we demonstrated that the escape of human colonic epithelial cells from chronic inflammation-induced senescence lied on the activation of a specific genetic program.

overall_design: Immortalized human colonic epithelial cells (HCEC-hTERT) submitted to a chronic inflammation commit into a senescence program, until cells resume proliferation. We compared the gene expression profiles of the parental HCEC-hTERT cell line with cells that escaped from chronic inflammation-associated senescence, named Esc-Inf (from two independent experiments Esc-Inf A and Esc-Inf B) as well as HCEC-hTERT cells transduced with murine Zeb1 or Zeb2 (HCEC-Zeb1 and HCEC-Zeb2).

first: Stéphane

last: ANSIEAU

first: Guillaume

last: COLLIN

last: WIERINCKX

first: Séverine

last: CROZE


title: Gene expression analysis of hepatic stellate cells using Illumina HumanHT-12_V4 beadchip

city: Austin

first: Ningling

last: Kang

state: MN

address: 801 16th AVE NE

department: Hormel Institute

institute: University of Minnesota

summary: Human primary hepatic stellate cells were purchased from ScienCell Research Laboratories. To identify TGFβ transcription targets and those are also modulated by p300 acetyltransferase, cells were treated with C646 to inhibit p300 acetyltransferase or transduced with p300 shRNA to knockdown p300. Thus, cell were divided into 4 groups:  cells treated with DMSO, cells treated with C646 (15 uM), cells transduced with control shRNA, and cells transduced with p300 shRNA.  After cells were serum-starved, they were stimulated with or without TGF-beta for 24 hours.  Total RNA was then extracted and sent to University of Minnesota Genomic Center for microarray analysis.

overall_design: 8 RNA samples were submitted:  cell+DMSO, cell+DMSO+TGFβ, cell+C646, cell+C646+TGFβ; cell+conshRNA, cell+conshRNA+TGFβ, cell+p300shRNA, cell+p300shRNA+TGFβ


title: Three autoinducer molecules act synergistically to control virulence gene expression in Vibrio cholerae [dataset 1]

status: Public on Jun 25 2018

city: Jena

first: Kathrin

last: Fröhlich

state: Thuringia

address: Winzerlaer Straße 2

department: Fakultät für Biowissenschaften, Bacterial RNA Biology

institute: Friedrich-Schiller-Universität Jena

summary: Bacteria use quorum sensing (QS) to monitor cell density and coordinate group behaviours. In Vibrio cholerae, the causative agent of cholera disease, QS is linked to virulence gene expression via the autoinducer molecules, AI-2 and CAI-1. Both autoinducers share one signal transduction pathway to control AphA production, a key transcriptional activator of virulence genes. In this study, we demonstrate that the recently identified autoinducer, DPO, also controls AphA production in V. cholerae. DPO acts through the transcriptional activator, VqmA, and the VqmR small RNA to reduce AphA levels at the post-transcriptional level. Consequently, DPO inhibits virulence gene expression in V. cholerae, including repression of the cholera toxin, a key factor required for disease in humans. VqmR-mediated repression of AphA links the AI-2/CAI-1 and DPO-dependent QS pathways of V. cholerae and global transcriptome analysis indicate that all three autoinducers are required for full QS function. Together, our data provide the first view on autoinducer interplay in V. cholerae and highlight the importance of post-transcriptional gene regulation for collective functions in this major human pathogen.

overall_design: mRNA expression profiles of a V. cholerae strain deficient for autoinducer synthesis and induced with the corresponding autoinducers. Three independent biological replicates for each treatment with single autoinducers as well as all possible combinations are provided. The bacteria were grown in M9 minimal media in the presence of 5µM final concentration of the autoinducers: autoinducer 2 (AI-2), cholera-autoinducer-1 (CAI-1), or 3,5-dimethylpyrazin-2-ol (DPO), or water (control). The following day, bacteria were diluted 1:500 in fresh media with the same composition and RNA samples were collected at low optical density.

first: Roman

last: Herzog

first: Nikolai

last: Peschek

first: Kilian

last: Schumacher

first: Kai

last: Papenfort