title: BET bromodomain proteins Brd2, Brd3 and Brd4 selectively regulate metabolic pathways in the pancreatic β-cell

summary: Displacement of Bromodomain and Extra-Terminal (BET) proteins from chromatin has promise for cancer and inflammatory disease treatments, but roles of BET proteins in metabolic disease remain unexplored. Small molecule BET inhibitors, such as JQ1, block BET protein binding to acetylated lysines, but lack selectivity within the BET family (Brd2, Brd3, Brd4, Brdt), making it difficult to disentangle contributions of each family member to transcriptional and cellular outcomes. Here, we demonstrate multiple improvements in pancreatic β-cells upon BET inhibition with JQ1 or BET-specific siRNAs. JQ1 (50-400 nM) increases insulin secretion from INS-1 cells in a concentration dependent manner. JQ1 increases insulin content in INS-1 cells, accounting for increased secretion, in both rat and human islets. Higher concentrations of JQ1 decrease intracellular triglyceride stores in INS-1 cells, a result of increased fatty acid oxidation. Specific inhibition of both Brd2 and Brd4 enhances insulin transcription, leading to increased insulin content. Inhibition of Brd2 alone increases fatty acid oxidation. Overlapping yet discrete roles for individual BET proteins in metabolic regulation suggest new isoform-selective BET inhibitors may be useful to treat insulin resistant/diabetic patients. Results imply that cancer and diseases of chronic inflammation or disordered metabolism are related through shared chromatin regulatory mechanisms.

overall_design: BET proteins are not redundant in their functions, thus pan-BET inhibitors like JQ1 cannot properly be interpreted without specific RNA knockdown or small molecules of proven selectivity. Here, we expose INS-1 cells, a rat insulinoma model for the pancreatic beta cell, to selective siRNAs to ablate Brd2, Brd3 or Brd4 mRNAs and compared genome-wide changes in transcription to non-targeted siRNA control. As expected, three resolvably different patterns of gene expression were identified, establishing that each BET protein controls its own set of target genes.

first: Gerald

last: Denis

first: Jude

last: Deeney

first: Barbara

last: Corkey


title: Master transcription factors in corneal epithelial cells [OVOL2 transduced experimental samples]

status: Public on Apr 11 2016

city: Kyoto

first: Koji

last: Kitazawa

state: Kyoto

address: 465 Kajiicho Kamigyoku

department: Ophthalmology

country: Japan

institute: Kyoto Prefectural University of Medicine

summary: In development, embryonic ectoderm differentiates into several lineages including neuroectoderm and surface ectoderm, through the mechanism largely unclear. Here we report that OVOL2 is required for the transcriptional program of corneal epithelium cell(CEC)s, a derivative of surface ectoderm, and it might regulates the differential transcriptional programs between the two lineages. By a functional screening, we identified transcription factors (TFs) maintaining human CECs. OVOL2 was necessary to maintain the transcriptional program in CECs, particularly through repressing expression of mesenchymal genes. OVOL2 combined with several TFs were able to activate the transcriptional program of CECs in fibroblasts, accompanied by induction of chromatin landscape. Moreover, our analysis revealed that neuroectoderm derivatives express some of mesenchymal genes. In fact, OVOL2 alone was able to induce the transcriptional program of CECs in neural progenitor cells (NPCs) through repression of mesenchymal genes as well as activation of epithelial genes. Our data suggest that the difference between the transcriptional programs of surface ectoderm-derivatives and neuroectoderm-derivatives is regulated in part by the reciprocally-repressive mechanism between epithelial and mesenchymal genes that is seen in epithelial-to-mesenchymal transition.

overall_design: Human in vivo samples; N=4, 6TFs transduced experimental samples; N=10, OVOL2 transduced experimental samples; N=4

first: Shigeru

last: Kinoshita

first: Shinji

last: Masui


title: Locally Advanced Rectal Cancer - Radiation Response Prediction Study - Serum Proteins

status: Public on Apr 21 2016

city: Lørenskog

first: Anne

middle: Hansen

last: Ree

address: Sykehusveien 25

department: Division of Medicine - Oncology

country: Norway

institute: Akershus University Hospital

summary: The study objective was to find new biomarkers of treatment response and adverse events in patients receiving neoadjuvant therapy for locally advanced rectal cancer. Patients received neoadjuvant chemotherapy (NACT) followed by chemoradiotherapy (CRT) and underwent treatment evaluation four weeks after CRT completion. Radical pelvic surgery was planned 2-4 weeks later. Patients were scored for treatment adverse events, according to Common Terminology Criteria for Adverse Events (CTCAE) version 3.0, throughout the neoadjuvant treatment course, including at NACT and CRT completion. Treatment response was assessed by histologic ypTN staging and tumor regression grade (TRG) scoring, as well as progression-free survival (time from Inclusion date to Date of local relapse or Date of metastatic disease, whichever came first) recorded for five years after surgery.

overall_design: From 80 study patients, serial serum samples were collected at baseline (Sampling point=1), following NACT (post-NACT; Sampling point=2), at CRT completion (post-CRT; Sampling point=4), and at treatment evaluation (Sampling point=5). The samples were analyzed with a high-density antiboly array (AHH-BLG-1; RayBiotech Inc.) for the presence of 507 proteins.

middle: H


title: Reconstructing genetic history of Siberian and Notheastern European populations

status: Public on Mar 22 2016

city: Los Angeles

first: Anton

last: Valouev

address: 1450 Biggy Street, NRT 2509K

country: USA

institute: University of Southern California

summary: To obtain a broad overview of the population genetic relationships, we genotyped 48 samples from the Mansi population and 48 samples from the Khanty population, and compared them to samples from 25 other populations.

overall_design: Genomic DNA extracted from blood was genotyped using HumanOmniExpress-12 v1-1 (the first set of 48 samples) and HumanOmniExpress-24 v1-0 (the second set of 48 samples) Genotyping BeadChips (Illumina).

first: Svetlana

last: Limborska


title: Differential expression of genes and protein networks in the primary breast tumor that proceed to distant metastasis

status: Public on Feb 10 2016

city: Bangalore

first: Neeraj

last: KUMAR

address: Indian Institute of Science Bangalore

department: MRDG

country: India

institute: Indian Institute of Science Bangalore

summary: The presence or absence of lymph node metastasis plays a major role in the prediction of prognosis and subsequent patient management. However, good proportion of patients who display lymph node positivity remain disease free for 3 years or more, after the initial treatment, while a third of those who were lymph node negative at presentation, develop distant metastasis within the same period. We performed gene expression profiling on a cohort Indian breast cancer patients  followed up for a period of 3-5 years and in comparison with a previously published Caucasian cohort data, we identified gene signatures that are associated with distant metastasis. This association was irrespective of the hormone receptor status. Our results show that the genes that signify immune system development and response are repressed, while factors for DNA replication are up regulated in patients who develop distant metastasis. A large number of genes encoding proteins involved in the mitotic spindle formation that belong to the TRIM28 protein network, are differentially regulated in the metastatic tumors. Also, there was a significant overlap of genes reported in a mouse model of bone metastasis, with patients who developed bone metastasis in our cohort.  In conclusion, we present for the first time probable gene signatures that correlate with distant metastasis in breast cancer patients irrespective of nodal or hormone receptor status

overall_design: 80 indian breast cancer patients(samples),comprising of 22ER+(estrogen receptor),and 55 ER-.PR(progesterone receptor) ,HER and NOD status are also given in corresponding sample title and array files

first: Paturu

last: Kondaiah

first: Surekha

last: Damineni

first: NEERAJ


title: Identification of SDPR as a metastasis suppressor gene

status: Public on Feb 02 2016

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary:
To identify metastasis suppressor genes, which are functionally compromised in late-stage breast cancer, we compared the gene expression profiles of an established breast cancer progression cell line model and leveraged large amounts of publically available data by applying multiple bioinformatics filters. Here we report the identification of serum deprivation response (SDPR, also known as cavin-2) as a bona fide metastasis suppressor, capable of impairing the metastatic growth of cancer cells while having no effect on the growth of primary tumors.
Breast cancer cell lines representing progressive stages of the disease are compared by microarrays to find the genes repressed at the metastatic stage.

overall_design: Three cell lines, MCF-10AT1Kcl2 (MII - carcinoma in situ), MCF-10A1h (MIII - carcinoma) and MCF-10A1a (MIV - carcinoma, metastatic), are chosen to extract mRNA and hybridization with Affymetrix microarrays to establish the list of the genes that are lost in metastatic MIV breast cancer cell line.

first: Sait

last: Ozturk

first: Panagiotis

last: Papageorgis

first: Arthur

middle: W

last: Lambert

first: Hamid

middle: M

last: Abdolmaleky

first: Arunthathi

last: Thiagalingam

first: Herbert

middle: T

last: Cohen

first: Sam


title: Master transcription factors in corneal epithelial cells [in vivo samples]

first: Koji

overall_design: Human in vivo samples; N=4, 6TFs transduced experiments; N=10, OVOL2 transduced experiments; N=4

first: Shigeru


title: Chip-Seq analysis of HAUSP and HIF-1alpha

status: Public on Jan 13 2016

city: Taoyuang

first: Kou-Juey

last: Wu

state: Taiwan

address: No.15, Wenhua 1st Road, Gueishan Dist

department: Cancer Genome Research Center

country: Taiwan

institute: Chang Gung Memorial Hospital at Linkou

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We reported that HAUSP (USP7) deubiquitinase interacts with and deubiquitinates HIF-1α to increase  its stability and functions. HAUSP, HIF-1alpha and CBP could form a complex to regulate histone modification and gene transcription

overall_design: To identify the overlapping set of genes bound by HAUSP and HIF-1alpha, (1) H1299 and MDA-MB 231 cells were used for Chip-seq analysis of HAUSP, (2) H1299 cells lysate was used for Chip-seq analys of HIF-1alpha, and (3) H1299 cell as an input

first: H

first: Y

middle: K

last: Kuo

first: W

middle: C

last: Cheng

first: K

middle: J


title: Germline loss of PKM2 promotes metabolic distress and hepatocellular carcinoma

status: Public on Mar 25 2016

city: Cambridge

first: A

last: Bhutkar

address: 77 Massachusetts Avenue

institute: MIT

type: Expression profiling by high throughput sequencing

summary: Alternative splicing of the Pkm gene product generates the PKM1 and PKM2 isoforms of pyruvate kinase, and PKM2 expression is closely linked to embryogenesis, tissue regeneration, and cancer. To interrogate the functional requirement for PKM2 during development and tissue homeostasis, we generated germline PKM2 null mice (Pkm2-/-). Unexpectedly, despite being the primary isoform expressed in most wild-type adult tissues, we found that Pkm2-/- mice are viable and fertile. Thus, PKM2 is not required for embryonic or postnatal development. Loss of PKM2 leads to compensatory expression of PKM1 in the tissues that normally express PKM2. Strikingly, PKM2 loss leads to spontaneous development of hepatocellular carcinoma (HCC) with high penetrance that is accompanied by progressive changes in systemic metabolism characterized by altered systemic glucose homeostasis, inflammation, and hepatic steatosis. Therefore, in addition to its role in cancer metabolism, PKM2 plays a role in controlling systemic metabolic homeostasis and inflammation, thereby preventing HCC by a non-cell-autonomous mechanism.

overall_design: RNA was isolated from flash frozen ground whole liver tissue of 35 week old PKM2 KO and WT mice. Three independent mice from each condition were used as biological replicates.

first: Talya

middle: L

last: Dayton

first: Vasilena

last: Gocheva

first: Kathryn

last: Miller

first: William

last: Israelsen

first: Arjun

first: Shawn

last: Davidson

first: Clary

middle: B

last: Clish

first: Roderick

last: Bronson

first: Tyler

last: Jacks

first: Matthew

middle: G

last: Vander Heiden


title: miRNA expression data from the hearts of murine myocardial infarction model

status: Public on Jan 07 2016

city: Bunkyo

first: Masato

last: Tsuji

department: Biological Sciences

institute: The University of Tokyo

summary:
Sexual dimorphisms are well recognized in various cardiac diseases, including myocardial infarction (MI). MI develops later in women, but once established, it contributes more persistent symptoms and higher mortality than in men. Similar observations have been reported in murine model of MI. Although mRNA-level sexual dimorphism of MI have been reported, whether miRNA transcriptome also confers such dimorphism remains unknown. Comprehensive understanding of the mRNA- and miRNA-level genetic programs underlying the heart sexual dimorphisms will expectedly improve clinical outcome by facilitating the development of gender specific treatment strategies.
Here, by conducting miRNA microarray analysis of murine MI model samples, we set out to characterize the heart sexual dimorphisms at the level of miRNA transcriptome

overall_design: The left anterior descending (LAD) coronary artery of mice aged 10 weeks was surgically ligated to create extensive MI. The ventricular septum of the areas at risk of ischemia was sampled on post-operative day 28. Total RNA was extracted using Sepasol solution (Sepasol-RNA I super G, nakalai tesque, Japan), and microarray analysis was performed using Affymetrix GeneChip® miRNA 3.0 Arrays

first: Tomonori

last: Kawasaki

first: Tamaki

last: Morishita

first: Satoshi

last: Gojo

first: Jun

last: Takeuchi


title: DNA methylation data from CNS-PNETs and various other brain tumor samples

status: Public on Feb 25 2016

first: Volker

last: Hovestadt

address: 360 Longwood Avenue

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

type: Methylation profiling by genome tiling array

summary: Primitive neuroectodermal tumours of the central nervous system (CNS PNETs) are highly aggressive, poorly differentiated embryonal tumours occurring predominantly in young children. Using DNA methylation and gene expression profiling we have demonstrated that a significant proportion of institutionally diagnosed CNS PNETs display molecular profiles indistinguishable from those of various other well defined CNS tumour entities, facilitating diagnosis and appropiate therapy for children with these tumours. From the remaining fraction of CNS PNETs, we have identified four distinct new CNS tumour entities extending to other neuroepithelial tumours, each associated with a recurrent genetic alteration and particular histopathological and clinical features. These molecular entities, designated “CNS Neuroblastoma with FOXR2 activation (CNS NB FOXR2)”, “CNS Ewing sarcoma family tumour with CIC alteration (CNS EFT CIC)”, “CNS high grade neuroepithelial tumour with MN1 alteration (CNS HGNET MN1)”, and “CNS high grade neuroepithelial tumour with BCOR alteration (CNS HGNET BCOR)”, will enable meaningful clinical trials and the development of therapeutic strategies for patients affected by these poorly differentiated CNS tumours.

overall_design: 586 brain tumor samples were profiled using the Illumina HumanMethylation450 BeadChip (450k) array.

first: Dominik

last: Sturm

first: Marcel

last: Kool


title: E2F1 orchestrates transcriptomics and oxidative metabolism in Wharton’s jelly derived mesenchymal stem cells from growth-restricted neonates

status: Public on Jan 28 2016

city: Singapore

first: Walter

last: Stunkel

address: 30 Medical Drive, Brenner Centre Lvl 4

country: Singapore

institute: Singapore Institute for Clinical Sciences

summary: Wharton’s jelly derived Mesenchymal Stem Cells (MSCs) isolated from newborns with intrauterine fetal growth restriction were previously shown to exert anabolic features including insulin hypersensitivity. Here, we extend these observations and demonstrate that MSCs from small for gestational age (SGA) individuals have decreased mitochondrial oxygen consumption rates. Comparing normally grown and SGA MSCs using next generation sequencing studies, we measured global transcriptomic and epigenetic profiles and identified in SGA, E2F1 as an over-expressed transcription factor regulating oxidative metabolism. We further show that E2F1 regulates the differential transcriptome found in SGA and is associated with the activating histone marks H3K27ac and H3K4me3. One of the key genes regulated by E2F1 was found to be the fatty acid elongase ELOVL2, a gene involved in the endogenous synthesis of docosahexaenoic acid (DHA).

overall_design: ChIP-seq of E2F1, H3K27ac, H3K27me3, H3K36me3, H3K4me1 and H3K4me3 in MSCs from 3 AGA and 3 SGA samples. RNA-seq of basal, siCTRL and siE2F1 conditions in the same 6 MSC lines.

first: Peck

middle: Y

last: Tan

first: Cheng

last: Chang

first: Kaibo

last: Duan

first: Michael

last: Poidinger

first: Kai

last: Ng

first: Yap

middle: S

last: Chong

first: Peter

middle: D

last: Gluckman

last: Stünkel


title: RNA-Seq to assess the transcriptional effects of G quadruplex stabilization by the G4 ligand PhenDC3 in HT-1080 cells

status: Public on Jan 31 2016

city: Seattle

first: Lucas

last: Gray

state: WA

address: 615 Westlake Ave N

department: Molecular Genetics

institute: Allen Institute for Brain Science

summary:
G-quadruplex motifs are frequently located near TSS and in the first introns of transcribed genes. We investigated the role that G4 structures play in transcription by stabilizing G4 DNA with the selective G4 ligand PhenDC3 in the HT-1080 human fibrosarcoma cell line. After treatment of triplicate samples with PhenDC3 or a negative control (DMSO carrier only), we performed RNA-Seq after poly-dT selection to assess changes in gene expression.

Heme is an essential cofactor for many enzymes, but free heme is toxic and its levels are tightly regulated. G-quadruplexes bind heme avidly in vitro, raising the possibility that they may sequester heme in vivo. If so, then treatment that displaces heme from quadruplexes is predicted to induce expression of genes involved in iron and heme homeostasis. Here we show that PhenDC3, a G-quadruplex ligand structurally unrelated to heme, displaces quadruplex-bound heme in vitro and alters transcription in cultured human cells, up-regulating genes that support heme degradation and iron homeostasis, and most strikingly causing a 30-fold induction of heme oxidase 1, the key enzyme in heme degradation. We propose that G-quadruplexes sequester heme to protect cells from the pathophysiological consequences of free heme. This identifies a new function for G-quadruplexes and a new mechanism for protection of cells from heme.

overall_design: 6 samples total; 2 gene expression conditions (treated and untreated) in triplicate; 4 raw sequencing files per sample

first: Nancy

last: Maizels

first: Emilia

last: Puig Lombardi


title: The Solanum lycopersicum WRKY3 Transcription Factor Regulates Salt Stress Tolerance In Tomato

status: Public on Mar 15 2016

city: Louvain-La-Neuve

first: IMENE

last: HICHRI

address: 5 (Bte 7.07.13) Place Croix du Sud

country: Belgium

institute: UCL

summary: The tomato SlWRKY3 transcription factor was overexpressed in cultivated tomato (Solanum lycopersicum)and transgenic plants transcriptome was compared to that of wild-type plants.

overall_design: At least 4 plants were collected for RNA extraction. The aim of the experiment was to compare transcriptomes of 35::SlWRKY3 plants and wild-type plants grown together and on MS (Murashige and Skoog) medium in vitro for 4 weeks. A technical replicate (dye swap) was conducted.

first: Imène

last: Hichri

first: Yordan

last: Muhovski

first: Eva

last: Žižková

first: Petre

middle: I

last: Dobrev

first: Emna

last: Gharbi

first: Jose

last: Franco-Zorrilla

first: Irene

last: Lopez-Vidriero

first: Roberto

last: Solano

first: André

last: Clippe

first: Abdelmounaim

last: Errachid

first: Vaclav

last: Motyka

first: Stanley

last: Lutts


title: small RNAseq in donor BMDCs and BMDCs that received exosomes

status: Public on Jan 01 2016

city: Salt lake city

first: Ryan

last: O'Connell

state: UT

address: 15 N Medical Dr East

department: Pathology

institute: University of Utah

type: Non-coding RNA profiling by high throughput sequencing

summary: small RNAseq was preformed on Wt bone marrow-derived dendritic cells (BMDC) and miR-155 and miR-146a double knockout (DKO)  BMDCs that received Wt exosomes to investigate the differences in transferred miRNA

overall_design: Small RNA profiles were generated from Wt donor BMDCs and DKO BMDCs given Wt exosomes 3 replicates in each group

first: Margaret

middle: R

last: Alexander


title: Alternative RNA processing events in a double NSR mutant Arabidopsis

city: Orsay

first: souiai

last: oussema

address: 15, rue Georges Clémenceau -

department: IGM

country: France

institute: CNRS

summary: We analyze the effect of a double deletion mutant for alternative-splicing regulators nsra and nsrb (Nuclear Speckle RNA binding proteins), on the Arabidopsis thaliana transcriptome.

overall_design: RNA-seq experiments (polyA+ RNA) in triplicates for each condition WT and nsrab mutants.

first: Natali

last: Romero-Barrios

first: Van

last: Tran

first: Oussema

last: Souiai

first: Daniel

last: Gautheret

first: Martin

last: Crespi


title: Mouse intestinal crypt epithelial cells: Apc+/Δ716 mice vs. Apc+/Δ716 Id2-/- compound mutant mice

status: Public on Mar 01 2016

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: Transcriptional profiling of mouse intestinal crypt epithelial cells comparing Apc+/Δ716 mice with Apc+/Δ716 Id2-/- mice.

overall_design: One-condition experiment, Apc+/Δ716 mice vs. Apc+/Δ716 Id2-/- mice, Biological replicates: 1 pooled intestinal crypt epithelium from 3 Apc+/Δ716 mice, 1 pooled intestinal crypt epithelium from 3 Apc+/Δ716 Id2-/- mice. One replicate per array.

first: Biyajima

last: Kyoko


title: Gene expression influenced by human APE1 and mouse Ape1 in a mouse embryonic fibroblast line.

city: Lexington

first: Tadahide

last: Izumi

state: KY

address: 1095 VA Dr

department: Toxicology

institute: University of Kentucky

summary: APE1 (AP-endonuclease 1) is an essential DNA repair protein but also it functions as a gene regulatory protein. A unique mouse embyonic fibroblast with almost undetectable levels of APE1 was isolated. Three isogenic derivatives of this cell line that contain either of the control vector, the human APE1 cDNA, and mouse Ape1 cDNA were analyzed for their global gene expression using Affymetrix mouse ST 2.0 chip set.

overall_design:
An important question that we wished to ask was how clusters of genes categorized based on the cellular activities (e.g., glycolysis, cell cycle) are regulated by the hAPE1 and mApe1. Because of the high amino acid sequence similarity between the human and mouse APE1 (94% identical), the two proteins are expected to influence the globl gene expression similarly.

Total RNA from a unique mouse embryonic fibroblast (MEF) line whose Ape1 expression is extremely low (0.2% of normal MEF). This is due to its genetic manipulation by transgenic procedures. The genotype of the APE1 gene in the MEF is mApe1-/- and hAPE1 transgenic (hAPE1TG). Mice used in this study were isogenic to C56BL/6.

first: Rangaswamy

last: Suganya


title: miRNA expression data from human myocardial infarction hearts

first: Masato

last: Tsuji

summary:
Sexual dimorphisms are well recognized in various cardiac diseases, including myocardial infarction (MI). MI develops later in women, but once established, it contributes more persistent symptoms and higher mortality than in men. Although mRNA-level sexual dimorphism of MI have been reported, whether miRNA transcriptome also confers such dimorphism remains unknown. Comprehensive understanding of the mRNA- and miRNA-level genetic programs underlying the heart sexual dimorphisms will expectedly improve clinical outcome by facilitating the development of gender specific treatment strategies.
Here, by conducting miRNA microarray analysis of human MI samples, we set out to characterize the heart sexual dimorphisms at the level of miRNA transcriptome

overall_design: Human tissue samples, acquired during post-mortem examination and frozen in liquid nitrogen, were provided by the department of pathology, Tokyo Metropolitan Geriatric Hospital after the approval from the ethical committee. Age- and sex-matched cohorts were selected to compare healthy hearts to those with post-MI LV remodeling. Border zone for myocardial infarction was sampled. Total RNA was extracted using Sepasol solution (Sepasol-RNA I super G, nakalai tesque, Japan), and microarray analysis was performed using Affymetrix GeneChip® miRNA 3.0 Arrays

first: Tomobori

last: Kawasaki

first: Tamaki

last: Morishita

last: Gojo

first: Jun

last: Takeuchi


title: miRNA expression data from the hearts of myocardial infarction model

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

sample_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Effect of pharmacological inhibition of ASBT on bile composition and sclerosing cholangitis in mdr2 knockout mice

status: Public on Feb 17 2016

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

summary: We report the effect of a potent pharmacological inhibition of ASBT in mdr2 -/- mice, compared to genetic and treatment controls using RNA-sequencing.  Through quantification of mRNA in liver samples, we found significant upregulation of anti-inflammatory and anti-fibrotic gene signatures in mdr2-/- mice. Additionally, we report downregulation of pro-inflammatory genes invovled in leukocyte recruitment.

overall_design: Mdr2 knockout mice (female, 30 day old) were fed high fat-chow diet containing a potent inhibitor of ASBT for 14 days.  Genotypic and dietary controls were included. RNA-sequencing was performed on liver samples taken from the caudate lobe.

first: Alex

last: Miethke


title: D9, a novel 3-Deazaneplanocin A (DZNep) analog, is efficacious in targeting acute myeloid leukemia (AML) (Sensitive vs Resistance)

status: Public on Dec 31 2015

city: Singpapore

first: Xia

last: Jiang

address: 60 Biopolis Street, #02-01, Genome, Singapore

institute: Genome Institute of Singapore

summary: We and others have previously reported that 3-Deazaneplanocin A (DZNep) is a histone methylation inhibitor that has a wide range anticancer effects in a variety of human cancers. Here, using acute myeloid leukemia as a model, we reported a less toxic analog of DZNep, named D9, that is shown to be efficacious in both cell lines and patient samples of AML. Gene expression analysis in a panel of AML cell lines treated with D9 identified a set of genes that is associated with D9 sensitivity and is implicated in multiple oncogenic signaling pathways. Moreover, we show that D9 is able to deplete the leukemia stem cells (LSC) and abolish chemotherapy-induced LSC enrichment, leading to dramatic elimination of AML cell survival and associated gene expression when combined with chemotherapy.  Thus, D9 appears to be a robust epigenetic compound that may constitute a potential for AML therapy.

overall_design: We evaluated the overall effects of D9 on histone lysine methylations in AML cell lines and its relationship to apoptosis induction by D9. The results demonstrated that the both sensitive and resistant cell lines, treated with D9 for 48 and 72 hours, showed similar levels of suppression of histone lysine methylation. Thus, the differential sensitivities of AML cells to D9 is not due to its different ability to inhibit the bulk histone methylation but is more likely to be associated with the differential gene expression response to D9. To test this hypothesis, we treated three sensitive (MOLM-14, MV4-11 and TF-1) and three resistant (Mono-Mac-1, THP-1, and KG-1a) cell lines with D9 at 1 or 5 μM for 48 hours and performed Illumina BeadChip transcriptom profiling analysis. Significance Analysis of Microarrays (SAM) analysis shows that D9 treatment resulted in transcriptional changes of 547 genes, including 327 upregulated genes and 220 downregulated genes in sensitive cell lines but not in resistant cell lines.

first: Jiang

last: Xia

first: Yu

last: Qiang


title: In-depth analysis of microRNA in bat hibernating regulation

city: Guangzhou

first: Lihong

last: Yuan

state: Guangdong

address: 105 Xin-gang Xi road

country: China

institute: Guangdong Entomological Institute

summary: We report the application of the Illumina/Solexa sequencing-by-synthesis platform to identify microRNA, which invovled in bat hibernating regualtion, in brain and adipose tissue. Total 866 microRNAs (including 477 novels) were identified and 269 microRNAs showed significant expression differences during hibernation, including 183 in brain and 199 in adipose tissue. Expressed pattern analysis indicated that two-thirds of differential expressed microRNAs showed down-regulated during hibernation in both tissues. This study will provide clules to in-deep analysis the molecular mechanism of hibernating regualtion.

overall_design: Identification of microRNA on hibernating regulation in 2 different tissues and 2 physiological states of bat.

first: Haibo

last: Sun

first: Benfu

last: Lin

first: Shuyi

last: Zhang


title: Comparative transcriptome profiling of a rice line carrying Xa39 and its parents triggered by Xanthomonas oryzae pv. oryzae provides novel insights into the broad-spectrum hypersensitive response

status: Public on Dec 30 2015

city: Beijing

first: Fan

state: Beijing

address: 12 South Zhong-Guan-Cun St.

institute: CAAS

summary:
To dissect the molecular mechanisms of resistance mediated by Xa39,the transcriptome profiling of a rice line carrying Xa39 and its parents at the early stage of Xoo infection were investigated.
A rice introgression line H471 carrying Xa39 exhibited a typical local hypersensitive response phenotype, accompanied by programmed cell death after inoculation with the Xoo Philippines’ race 9b.Our results indicated there might be cross-talk between the Xa39-mediated signal transduction cascades and the GA/BR signaling pathway, and the defense mechanism was related to diverse kinases, transcription factors, post-translational regulation, and R genes.

overall_design: Transcriptome profiling of H471 and its parents (HHZ and P28) at 1 and 2 days post-inoculation was performed using RNA sequencing.

first: Liyu

last: Huang

first: Yongli

last: Zhou


title: Host/microbial cross-talk in the gut: In-depth investigation of the symbiotic effects of Roseburia hominis

status: Public on Feb 05 2016

city: Aberdeen

first: Denise

last: Kelly

address: Institute of Medical Sciences

country: United Kingdom

institute: University of Aberdeen

summary: Here, we report analysis of both the bacterial and host transcriptome as affected by colonization of R. hominis in the mouse gut. Microbial genes required for colonization and adaptation in the murine gut, as well as host genes responding to colonization by this bacterial species, were uncovered.

overall_design: Germ-free (GF) male mice were gavaged at 0d with 100 uL of  R. hominis culture. Mice were sacrificed on 14d and 28d post-colonization in parallel to age-matched GF controls.

first: Imke

last: Mulder


title: Expression data from tomato (Solanum lycopersicum) plants in interaction with different Trichoderma strains

status: Public on Dec 25 2015

city: Salamanca

first: Enrique

last: Monte

state: Salamanca

address: Rio Duero

department: Spanish-Portuguese Centre for Agricultural Research

country: Spain

institute: University of Salamanca

summary:
Trichoderma harzianum T34 is a fungal strain able to promote the plant growth and to increase plant defense responses. Trichoderma harzianum transformants expressing the amdS gene, encoding an acetamidase, of Aspergillus nidulans produce a higher plant development than the wild type T34.
We used microarrays to analyze the physiological and biochemical changes in tomato plants produced as consequence of interaction with Trichoderma harzianum T34 and amdS transformants

overall_design: Aerial parts of tomato plants in interaction with different Trichoderma strains were selected for RNA extraction and hybridization on Affimetrix microarrays

first: M

last: Rubio

first: Sara

last: Dominguez


title: D9, a novel 3-Deazaneplanocin A (DZNep) analog, is efficacious in targeting acute myeloid leukemia (AML) (Chemotherapy)

overall_design: We found D9 treatment depleted chemotherapy-induced LSC. We next sought to characterize the molecular changes induce by the chemotherapy that is antagonized by D9. To do this, TF-1a cells before and after Ara-C or ADR treatment or co-treated with D9 were harvested for RNA isolation and genome-wide transcription profilling.


title: Rapid evolutionary adaptation to growth on an ‘unfamiliar’ carbon source

status: Public on Dec 17 2015

city: Los Angeles

first: Zvi

last: Tamari

state: California

address: 5531 Boelter Hall

institute: UCLA

summary: Cells constantly adapt to changes in their environment. In the majority of cases, the environment shifts between conditions that were previously encountered during the course of evolution, thus enabling evolutionary-programmed responses. In rare cases, however, cells may encounter a new environment to which a novel response is required. To characterize the first steps in adaptation to a novel condition, we studied budding yeast growth on xylulose, a sugar that is very rarely found in the wild. We previously reported that growth on xylulose induces the expression of amino-acid biosynthesis genes, in multiple natural yeast isolates. This induction occurs despite the presence of amino acids in the growth medium and is a unique response to xylulose, not triggered by any of the naturally available carbon sources tested. Propagating these strains for ~300 generations on xylulose significantly improved their growth rate. Notably, the most significant change in gene expression was the loss of amino acid biosynthesis gene induction. Furthermore, the reduction in amino-acid biosynthesis gene expression on xylulose was strongly correlated with the improvement in growth rate, suggesting that internal depletion of amino-acids presented the major bottleneck limiting growth in xylulose. We discuss the possible implications of our results for explaining how cells maintain the balance between supply and demand of amino acids during growth in evolutionary ‘familiar’ vs. ‘novel’ conditions.

overall_design: mRNA profiles of 12 wt S. cerevisiae strains grown on either YPD or YP-xylulose, before and after 300 generations evolution on YP-xylulose

first: Naama

last: Barkai


title: To find out lncRNAs contribute to the development of gallbladder cancer

status: Public on Jan 08 2016

city: Shanghai

first: Huaifeng

last: Li

address: NO.1665, kongjiang road, Shanghai, China

department: general surgery

institute: Xinhua hospital affiliated to Shanghai jiaotong university, school of medicine

summary: To further understand the molecular mechanisms in the development of gallbladder cancer, we employed this microarray to identify lncRNAs associated with gallbladder cancer.

overall_design: 9 pairs of  gallbladder cancer tissues and paired normal gallbladder tissues were collected after colecystectomy.

first: Ying-bin

last: Liu

first: Shu-han

first: Xiang-song

last: Wu

first: Fang

last: Wang

first: Wei

last: Gong

first: Yun-ping

last: Hu

first: Huai-feng

first: Lin

first: Mao-lan

first: Xu-an

first: Fei

first: Shan-shan

last: Xiang

first: Yuan-yuan

last: Ye

first: Jian

first: Yi-jian


title: Paclitaxel resistance in ovarian cancer increases oncolytic adenovirus efficacy via upregulated CAR expression and dysfunctional cell cycle control

status: Public on Dec 10 2015

city: London

first: Claude

last: Chelala

state: London

address: Charterhouse square

department: Institute of Cancer

institute: Barts & The London School of Medicine (QMUL)

summary: The microtubule-stabilising drug paclitaxel has activity in relapsed ovarian cancer.  However, resistance frequently develops.  Oncolytic adenoviruses are a novel cancer therapy, and replicate selectively within and lyse malignant cells, leading to productive infection of neighbouring cells.  We found increased efficacy of adenoviruses of multiple subtypes in paclitaxel-resistant ovarian cancer cells.  There was increased expression of a key adenovirus receptor, CAR (coxsackie adenovirus receptor), due to increased transcription that resulted from histone modification.  Moreover, CAR transcription increased in intraperitoneal xenografts with acquired paclitaxel resistance and in tumours from patients with paclitaxel-resistant ovarian cancer.  Finally, we identified dysregulated cell cycle control as a second mechanism of increased adenovirus efficacy in paclitaxel-resistant ovarian cancer and that inhibition of CDK4/6 using PD-0332991 was able both to reverse paclitaxel resistance and reduce adenovirus efficacy.  Thus, paclitaxel resistance increases oncolytic adenovirus efficacy via at least two separate mechanisms.

overall_design: Parental SKOV3 and paclitaxel-resistant SKOV3-TR cells were analysed in duplicate

first: Iain

last: McNeish


title: Genome-wide Ultrabithorax binding analysis reveals highly targeted genomic loci at developmental regulators and a potential connection to Polycomb-mediated regulation

city: Vienna

first: Daria

last: Shlyueva

address: Dr. Bohr-gasse,7

country: Austria

institute: IMP

summary: Hox homeodomain transcription factors are key regulators of animal development. They specify the identity of segments along the anterior-posterior body axis in metazoans by controlling the expression of diverse downstream targets, including transcription factors and signaling pathway components. The Drosophila melanogaster Hox factor Ultrabithorax (Ubx) directs the development of thoracic and abdominal segments and appendages, and loss of Ubx function can lead for example to the transformation of third thoracic segment appendages (e.g. halters) into second thoracic segment appendages (e.g. wings), resulting in a characteristic four-wing phenotype. Here we present a Drosophila melanogaster strain with a V5-epitope tagged Ubx allele, which we employed to obtain a high quality genome-wide map of Ubx binding sites using ChIP-seq. We confirm the sensitivity of the V5 ChIP-seq by recovering 7/8 of well-studied Ubx-dependent cis-regulatory regions. Moreover, we show that Ubx binding is predictive of enhancer activity as suggested by comparison with a genome-scale resource of in vivo tested enhancer candidates. We observed densely clustered Ubx binding sites at 12 extended genomic loci that included ANTP-C, BX-C, Polycomb complex genes, and other regulators and the clustered binding sites were frequently active enhancers. Furthermore, Ubx binding was detected at known Polycomb response elements (PREs) and was associated with significant enrichments of Pc and Pho ChIP signals in contrast to binding sites of other developmental TFs.  Together, our results show that Ubx targets developmental regulators via strongly clustered binding sites and allow us to hypothesize that regulation by Ubx might involve Polycomb group proteins to maintain specific regulatory states in cooperative or mutually exclusive fashion, an attractive model that combines two groups of proteins with prominent gene regulatory roles during animal development.

overall_design: Ubx was endogenously tagged with V5 epitope in Drosophila melanogaster (Ubx-V5). ChIP-seq was performed with chromatin from 0-16 hrs wild type and Ubx-V5 embryos. The samples  were subjected to single-end sequencing in two replicates.

first: Antonio

last: Meireles-Filho

first: Michaela

last: Pagani

first: Alexander

last: Stark


title: A Functionally Conserved Gene Regulatory Network Module Governing Olfactory Neuron Diversity

status: Public on Dec 16 2015

city: Chapel Hill

first: Corbin

last: Jones

state: NC

address: 250 Bell Tower

department: Biology

institute: University of North Carolina

summary: Sensory neuron diversity is required for organisms to decipher complex environmental cues. In Drosophila, olfactory environment is detected by 50 different olfactory receptor neuron (ORN) classes that are clustered in combinations within distinct sensilla subtypes. Each sensilla subtype houses stereotypically clustered 1-4 ORN identities that arise through asymmetric divisions from a single multipotent sensory organ precursor (SOP). How each class of SOPs acquires a unique differentiation potential that accounts for ORN diversity is unknown. Previously, we reported a critical component of SOP diversification program, Rotund (Rn), which functions to increase ORN diversity by generating novel developmental trajectories from existing precursors within each independent sensilla type lineages. Here, we show that Rn, along with BarH1/H2, Bric-à-brac (Bab), Apterous (Ap) and Dachshund (Dac), constitute a functionally conserved transcription factor (TF) network, previously shown to pattern the segmentation of the leg, that patterns the developing olfactory tissue. Precursors with diverse ORN differentiation potentials are selected from concentric rings defined by unique combinations of these TFs along the proximodistal axis of the developing antennal disc. The combinatorial code that demarcates each precursor field is set up by cross-regulatory interactions among different factors within the network. Modifications of this network lead to predictable changes in the diversity of sensilla subtypes and ORN pools. In light of our data, we propose a molecular map that defines

overall_design: Time-course RNAseq across 4 developmental stages, inlcuding flies mutant for rotund gene (rn), heterozygotes and wildtype

first: Qingyun

first: Scott

last: Barish

first: Sumie

last: Okuwa

first: Abigail

last: Maciejewski

first: Alicia

last: Brandt

first: Dominik

last: Reinhold

first: Pelin

last: Volkan


title: Germ cell sexual differentiation requires Nanos2-mediated repression of Dazl in mice [Set 2]

status: Public on Dec 01 2015

city: Mishima

first: Yuzuru

last: Kato

state: Shizuoka

address: 1111 Yata

department: Division of Mammalian Development

institute: National Institute of Genetics

summary: In mouse embryos, sex-specific differentiation of primordial germ cells (PGCs) begins with distinct cell cycle regulations: while PGCs in female (XX) gonads enter meiosis, PGCs in male (XY) gonads defer meiosis and arrest cell cycle1,2. The mitotic quiescence in XY gonads requires Nanos2, an evolutionarily conserved RNA-binding protein implicated in RNA degradation3-5; however, underlying mechanisms including the identity of its target mRNAs in vivo remain unknown. Here we show that Nanos2 negatively regulates Dazl (Deleted in azoospermia-like), a germline-specific gene encoding an RNA-binding protein that is implicated in translational control and meiotic initiation6,7. Comprehensive microarray analyses identified Dazl as one of the genes that were up-regulated in Nanos2-deficient XY gonads, but down-regulated in Nanos2-expressing XX gonads. Analysis of a BAC transgenic mouse line, in which the 3’UTR of Dazl can be removed by Flp-Frt recombination system, showed that repression of Dazl is likely achieved by the association of Nanos2 with Dazl’s 3’UTR. Elevated levels of Dazl expression in the transgenic XY PGCs resulted in abnormal progression of cell cycles including meiosis, reminiscent of the phenotype observed in Nanos2-/- XY gonads. This phenotype was suppressed by inhibiting retinoic acid (RA) signaling, suggesting that Nanos2 represses Dazl to prevent RA-induced cell cycle progression in XY PGCs. Furthermore, we show that a part of Nanos2-associated mRNAs, most of which are up-regulated in Nanos2-/- XY gonads, can also associate with Dazl, and that excess Dazl impedes localization of Nanos2 to processing-bodies where RNA degradation takes place, suggesting that repression of Dazl is required for Nanos2 to efficiently degrade its target mRNAs. These data provide the first link between the two RNA-binding proteins that play pivotal roles in sexual differentiation of murine PGCs.

overall_design: RNA-immunoprecipitation using anti-Dazl antibody

first: Kato

last: Yuzuru

first: Saga

last: Yumiko


title: Germ cell sexual differentiation requires Nanos2-mediated repression of Dazl in mice [Set 1]

overall_design: Ectopic induction of Nanos2 in XX PGCs. Duplicated control (Tg:CAG-CAT-3FlagNanos2-pA) and experiment (Tg:CAG-CAT-3FlagNanos2-pA and Tg:Oct4-CreERT2)


title: Microarray analysis of exogenous NAD+-induced transcriptome changes in Arabidopsis thaliana

status: Public on Jan 07 2016

city: Gainesville

first: Zhonglin

last: Mou

state: FL

address: 981 Museum Road

department: Microbiology and Cell Science & Plant Molecular and Cellular  Biology

institute: University of Florida

summary: The goal of the microarray was to investigate the transcriptome changes induced by exogenous NAD+ in the wild-type Col-0 plants. Results showed that exogenous NAD+-induced dramatic transcriptional changes in Arabidopsis. Particularly, a large group of salicylic acid pathway genes including NPR1 and its traget genes were induced by NAD+, whereas the jasmonic acid/ethylene pathway defense marker gene PDF1.2 was inhibited by NAD+ treatment. In addition, a group of the pathogen-associated molecular pattern pathway genes were also induced by exogenous NAD+. These results indicate that exogenous NAD+ induces defense pathways against (hemi)biotrophic pathogens but suppresses defense against necrotrophs.

overall_design: Two to three replicates with leaves from 8-12 plants per sample were collected at 0, 4, and 24 hr after NAD+ treatment. Leaf tissues were collected as the control at 0 hr, and NAD+-treated leaf tissues were collected at 4 and 24 hr.  After extraction, RNA concentration was determined on a NanoDrop Spectrophotometer (Thermofisher Scientific, Waltham, MA) and sample quality was assessed using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).  Equal amount of RNA from the biological replicates were used for microarray analysis.

first: Chenggang

last: Wang

first: Mingqi

last: Zhou

first: Xudong

last: Zhang

first: Jin

last: Yao

first: Yanping

first: Yijun

last: Sun


title: Haemophilus ducreyi transcriptome during human infection

status: Public on Nov 21 2015

city: Indianapolis

first: Dharanesh

last: Gangaiah

state: Indiana

address: 635 Barnhill drive, MS 420

department: Department of Microbiology and Immunology

institute: Indiana University School of Medicine

summary: To better understand the molecular mechanisms underlying Haemophilus ducreyi infection in humans, here we determined the transcriptional profile of H. ducreyi in human lesions using RNA-Seq and compared it to that of in vitro growth. We were able to show that the in vivo transcriptome did not resemble that of in vitro growth. Compared to the inoculum, H. ducreyi harvested from pustules differentially expressed ~120 genes, of which 68 were upregulated. A large proportion of the upregulated genes encoded homologs of proteins involved in nutrient transport, alternative carbon pathways, growth arrest response, heat shock response, and DNA recombination. H. ducreyi upregulated few genes or operons (hgbA, flp-tad, and lspB-lspA2) required for human infection; expression of these genes is known to increase under nutrient stress. Homologs of several genes involved in anaerobic metabolism and ascorbate utilization were upregulated in vivo, suggesting that the organism is adjusting its metabolism to anaerobiosis in vivo.

overall_design: RNA from Haemophilus ducreyi infected pustules were collected from four volunteers and performed RNA-Seq.

first: Stanley

last: Spinola


title: Growth-phase dependent gene regulation in the alpha-proteobacterium Rhodobacter sphaeroides

status: Public on Nov 26 2015

city: Gießen

first: Gabriele

last: Klug

address: Heinrich-Buff-Ring 26-32

department: Molecular- and Microbiology

country: Germany

institute: Justus-Liebig University Gießen

summary: Global transcriptome analyses at different stages of growth were applied to monitor growth phase-dependent gene expression in the alpha-proteobacterium Rhodobacter sphaeroides. Low aerated cultures with strong changes in levels of dissolved oxygen during growth, were compared to aerated cultures showing little variation in oxygen levels. Cells were in stationary phase for 12 h or for 57 h before dilution into fresh medium. The majority of genes (78-86%) were not differentially expressed across growth phases. Gene expression in outgrowth phase was strongly influenced by the length of the preceding stationary phase. After 57 h in stationary phase a much larger number of genes was induced after dilution, 39% of which are known to be controlled by the alternative sigma factors RpoHI and/or RpoHII. Growth experiments with mutant strains assign an important function in stationary phase and especially in outgrowth to these sigma factors and genes for both sigma factors showed growth phase-dependent expression. Besides the known consensus sequences for the RpoH sigma factors, some new consensus sequences were identified in subsets of growth phase-dependent genes. Genes for several predicted regulatory proteins exhibited growth phase-specific expression implying a role in growth phase adaptation in alpha-proteobacteria, which needs verification in the future.

overall_design:
RNA samples collected from R. sphaeroides 2.4.1 wild type cells in several growth phases were analyzed by two-color microarrays
Please note that each sample represents biological triplicates.

first: Bernhard

last: Remes


title: Long non-coding RNAs  in psoriatic and healthy skin

status: Public on Nov 17 2015

city: Dublin

first: Rashmi

last: Gupta

state: CALIFORNIA

address: 5529 Esprit Way

institute: UCSF

summary: In this study, we used RNA-sequencing to profile the long non-coding RNA (lncRNA) transcriptome in lesional skin from psoriasis patients before (PP) and after treatment (PT) with adalimumab and in normal skin from healthy individuals (NN). For this we sequenced total RNA from 18 psoriasis patients (before and after treatment) and 16 healthy controls. We created our own reference set of long non-coding RNAs by merging three long non-coding RNA reference data sets. The combined reference had 67,157 lncRNA transcripts with no overlaps. We identified differential expression of 971 lncRNAs between PP and NN, 157 between PP and PT, and 377 between PT and NN. Based on differentially expressed (DE) lncRNAs between PP and NN, we identified a molecular lncRNA signature that distinguishes psoriatic skin from healthy skin .

overall_design: We recruited 18 psoriatic patients in our study. We took 5 mm punch biopsies from the edge of a psoriatic plaque before treatment and after one month of treatment with adalimumab. The mean improvement in the PASI over this time period was 53.1%. We obtained sixteen normal skin samples (N=16) from healthy control surgical discard specimens.

first: Richard

last: Ahn

first: Kevin

last: Lai

first: Elizabeth

last: Mullins

first: Maya

last: Debbaneh

first: Michelle

last: Dimon

first: Sarah

last: Arron

first: Wilson

last: Liao


title: Development of gene expression signatures for ASC activated by LL-37

city: Seoul

first: Sa Ik

last: Bang

address: Ilwon-dong 50 cancer center

department: Plastic Surgery

country: South Korea

institute: Samsung Medical Center

summary: To further development of our gene expression approach to ASC-mediated regeneration, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish radiation dose across an exposure range relevant for medical decision-making in a radiological emergency.   Human peripheral blood from healthy donors was irradiated ex vivo, and a 74-gene consensus signature was identified that distinguished between four radiation doses (0.5, 2, 5 and 8 Gy) and control samples.  The same set of genes separated samples by exposure level at both six and 24 hours after treatment, with overlap evident only at the highest two doses (5 and 8 Gy).  Expression of five genes (CDKN1A, FDXR, SESN1, BBC3 and PHPT1) from this signature was quantified in the same RNA samples by real-time PCR, confirming low variability between donors as well as the predicted radiation response pattern.

overall_design: LL-37 induced gene expression in human ASCs was measured at 1 hours after exposure to doses of 0, 20 microgram/ml LL-37.

first: SaIk

first: Yoolhee

last: Yang


title: RNA Seq analysis of unchecked miR-998 expression in Drosophila melanogaster 3rd instar larval eye discs

status: Public on Nov 15 2015

city: Chicago

first: Mary

last: Truscott

state: IL

address: 900 S Ashland Ave, room 2356

department: Biochemistry and Molecular Genetics

institute: University of Illinois at Chicago

summary: The importance of the role of microRNAs in gene expression and disease is well recognized. However, what is less appreciated is that almost half of miRNA genes are organized in polycistronic clusters and are therefore co-expressed. The mir-11~998 cluster consists of two miRNAs, miR-11 and miR-998. Here, we describe a novel layer of regulation that links the processing and expression of miR-998 to the presence of the mir-11 gene. We show that the presence of mir-11 in the pri-miRNA is required for processing by Drosha, and deletion of mir-11 prevents the expression of miR-998. Replacing mir-11 with an unrelated miRNA rescued miR-998 expression in vivo and in vitro, as did expressing miR-998 from a shorter, more canonical miRNA scaffold. The embedded regulation of miR-998 is functionally important because unchecked miR-998 expression in the absence of miR-11 resulted in highly penetrant pleiotropic developmental defects. We further show that this novel regulation of expression of miRNAs within a cluster is not limited to the mir-11~998 cluster and likely reflects the more general cis-regulation of expression of individual miRNAs. Thus, our results reveal a novel layer of regulation within miRNA clusters that tempers the functions of the individual miRNAs. Unlinking their expression has the potential to change the expression of multiple miRNA targets and shift biological response.

overall_design: RNA was extracted from Drosophila third instar larval eye discs of animals grown in standard conditions; Illumina HiSeq2000 Next Gen RNA Sequencing was performed, and differential expression of genes was assessed in wild-type vs unchecked miR-998 expression

first: Abul

last: Islam

first: Max

last: Frolov


title: Expression data from stably-transfected KYSE150, transfected with shlncRNA625 or shscramble

status: Public on Nov 10 2015

city: Daqing

first: Chunquan

last: Li

address: School of Medical Informatics, Daqing Campus, Harbin Medical University

institute: Harbin Medical University

summary:
To delineate the putative biological functions for lncRNA625, We performed expression profile from stably-transfected KYSE150
transfected with shlncRNA625 or shscramble for functions of lncRNA625 in ESCC

overall_design: Stably-transfected KYSE150, transfected with shlncRNA625 or shscramble, were collected and lysed in TRIzol (Life technologies). Microarray experiments were performed following the Affymetrix protocol at the Shanghai Biotechnology Corporation.

first: Li-Yan

last: Xu

first: En-Min


title: Xenopus Piwi protein associated transcripts indicate regulation beyond transposons

city: BOSTON

first: NELSON

last: LAU

state: MA

address: 72 E Concord St K219, Dept of Biochemistry

department: Biochemistry and Cell Biology

institute: Boston University Chobanian & Avedisian School of Medicine

summary: This study examines the population of transcripts associated with the Xenopus Piwi proteins, Xiwi and Xili, from X.laevis and X.tropicalis. RIP-seq, CLIP-seq, piRNA-seq, and mRNA-seq datasets were integrated to determine how the Xenopus Piwi proteins where using piRNAs and binding interactions to associate with  transcripts in gonadal cells.

sample_organism:
Xenopus laevis
Xenopus tropicalis

platform_organism:
Xenopus laevis
Xenopus tropicalis

overall_design: We performed several replicates of a Piw CLIP-Seq experiment to isolate RNA fragments as CLIP-tags to discover which transcripts are preferentially bound by the Piwi protein.  Then we performed several types of mRNA expression profiling experiments using several forms of mRNA-Seq library construction formats.  Finally, we sequenced the piRNAs from the OSS cells

first: Trey

last: Toombs

first: Yuliya

last: Sytnkova

first: Gungwei

last: Chirn

first: Nelson

last: Lau

first: Michael

last: Blower


title: Differential alteration of the transcriptome upon plakophilin3 loss in HCT116 cell line

city: navi mumbai

first: Srikanta

last: Basu

state: Maharashtra

address: Kharghar, sector 22

department: Sorab's Lab

institute: TMC-ACTREC

summary: To understand alterations in gene expression upon plakophilin3 (PKP3) loss, we generated two HCT116 derived plakophilin3 knockdown clones. One of these clones named shpkp3-2 was used for the experiment. The gene expression profile of shpkp3-2 was compared with the vector control named vec.

overall_design: RNA used for this experiment was obtained from two biological replicates of vec (vec1 and vec2) and shpkp3-2 (shpkp3-2-1 and  shpkp3-2-2). RNA from the clones were obtained at separate time points in 2 groups. The first group was vec1 and shpkp3-2-1 and the second group was of  clones vec2 and shpkp3-2-2, respectively.

first: Sorab

middle: N

last: Dalal


title: Expression data from EP300 was subjected to knockdown by siRNA interference

summary: We knocked down EP300 and examined the expression of lncRNA625 target genes. Gene expression profiling of knockdown samples on cDNA microarrays indicated that EP300 affected expression of several lncRNA625 downstream target genes

first: Xu

last: Li-Yan

first: Li

last: En-Min


title: Gene expression analysis of BE(2)C cells treated with SSRP1 and MYCN siRNAs

status: Public on Nov 16 2015

city: Randwick

first: Daniel

last: Carter

address: Lowy Cancer Research Centre

country: Australia

institute: Children's Cancer Institute

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

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Germ cell sexual differentiation requires Nanos2-mediated repression of Dazl in mice

first: Yuzuru

last: Kato


title: Transcription of mammalian cis-regulatory elements is restrained by actively enforced early termination [ChIP-Seq]

status: Public on Nov 09 2015

first: Iros

last: Barozzi

address: Borschkegasse 8a

institute: Medical University Vienna

summary: Upon recruitment to active enhancers and promoters, RNA polymerase II (Pol_II) generates short non-coding transcripts of unclear function. The mechanisms that control the length and the amount of ncRNAs generated by cis-regulatory elements are largely unknown. Here, we show that the adapter protein WDR82 and its associated complexes actively limit such non-coding transcription. WDR82 targets the SET1/COMPASS H3K4 methyltransferase and the nuclear Protein Phosphatase 1 (PP1) complexes to the initiating Pol_II. WDR82 and PP1 also interact with components of the transcriptional termination and RNA processing machineries. Depletion of WDR82, SET1 or the PP1 subunit required for its nuclear import caused distinct but overlapping transcription termination defects at highly expressed genes, active enhancers and promoters, thus enabling the increased synthesis of unusually long ncRNAs. These data indicate that transcription initiated from cis-regulatory elements is tightly coordinated with termination mechanisms that impose the synthesis of short RNAs.

overall_design: Chromatin immunoprecipitations of H3 lysine 4 tri- or mono-methylated, H3 lysine 27 acetylated, H3 lysine 36 tri-methylated, total or CTD-serine 2 phosphorylated RNA polymerase II followed by multiparallel sequencing performed in murine bone marrow-derived macrophages (BMDMs). Experiments were carried out in cells containing either a short hairpin targeting Wdr82 or the empty vector (LMP) or a scrambled as a control. BMDMs were either untreated or treated for 4 hrs with lipopolysaccharide (LPS).

first: Liv

last: Austenaa

first: Marta

last: Simonatto

first: Silvia

last: Masella

first: Giulia

last: Della Chiara

first: Serena

last: Ghisletti

first: Alessia

last: Curina

first: Elzo

last: de Wit

first: Britta

middle: A

last: Bouwman

first: Stefano

last: de Pretis

first: Viviana

last: Piccolo

first: Alberto

last: Termanini

first: Elena

last: Prosperini

first: Mattia

last: Pelizzola

first: Wouter

last: de Laat

first: Gioacchino

last: Natoli


title: Comprehensive Identification of Long Non-coding RNAs in Purified Cell Types from the Brain Reveals Functional LncRNA in OPC Fate Determination (OLIG2 Chromatin immunoprecipitation sequencing (ChIP-Seq) in mouse neural stem cells)

status: Public on Nov 04 2015

city: houston

first: Xiaomin

last: Dong

state: Texas

address: 1825 Pressler Street

department: Department of neurosurgery

institute: UT health

summary: To better understand the OLIG2 binding site in the whole-genome of mouse neural stem cells, ChIP was performed using 107 mouse neural stem cells. The ChIP-Seq library was constructed by using DNA SMART ChIP-Seq Kit according to the manufacturer's instructions (Clontech) and was sequenced on the Illumina HiSeq 2000 Sequencer.

overall_design: OLIG2 Chromatin immunoprecipitation sequencing (ChIP-Seq) in mouse neural stem cell.

first: Raquel

last: Cuevas-Diaz Duran

first: Jia

middle: Q

last: Wu


title: Comprehensive Identification of Long Non-coding RNAs in Purified Cell Types from the Brain Reveals Functional LncRNA in OPC Fate Determination


title: Expression data from T-bet deficient megakaryoerythroid progenitor (MEP) cells

status: Public on Nov 01 2015

city: Baltimore

first: Arnob

last: Banerjee

state: MD

address: 20 Penn St

institute: University of Maryland Baltimore

summary: RNA was harvested from T-bet deficient MEP cells versus "wild type" C57BL/6 control MEP cells freshly harvested from bone marrow.

overall_design: 3 samples in each group, representing MEP cells from three different T-bet deficient or control mice.

first: Aki

last: Furusawa


title: Comprehensive Identification of Long Non-coding RNAs in Purified Cell Types from the Brain Reveals Functional LncRNA in OPC Fate Determination (RNA-Seq of mouse neural stem cells)

summary: To better understand the transcriptome of mouse neural stem cells (including known genes and novel long non coding RNA genes),  RNA-Seq was performed on the polyadenylated fraction of RNA isolated from cell samples. Read mapping and transcriptome construction were done by using optimized pipeline which integrate Tophat followed by Cufflinks.

overall_design: mRNA profiles of mouse neural stem cells were generated by RNA-sequencing.

first: Kenian

last: Chen


title: Comprehensive Identification of Long Non-coding RNAs in Purified Cell Types from the Brain Reveals Functional LncRNA in OPC Fate Determination (RNA-Seq of differentiated NSC after lnc-OPC knockdown)

summary: To quantitative analysis of transcriptome changes caused by lnc-OPC knockdown during OPC differentiation from NSC, lentivirus-based short hairpin RNAs were used to knockdown the lnc-OPC expression in a neural stem cell culture . Subsequently, puromycin-selected NSCs were differentiated to OPC in culture for three days.RNA-Seq was performed on the polyadenylated fraction of RNA isolated from cell samples. DEseq was used for differential gene expression analysis caused by lnc-OPC knockdown. GO functional term enrichment analysis of differential gene expression caused by lnc-OPC knockdown, revealed significant enrichment of ‘oligodendrocyte development’, ‘oligodendrocyte differentiation’, ‘glia cell development’, and ‘axon ensheathment’ terms that are associated with oligodendrogenesis.

overall_design: mRNA profiles of differentiiated NSC samples after lnc-OPC knockdown by RNA-sequencing.


title: Characterization of parental and rociletinib-resistant derived H1975 cell lines

status: Public on Nov 19 2015

city: San Francisco

first: Saurabh

last: Asthana

state: CA

address: 1450 Third Street, Room HD276

department: Helen Diller Family Comprehensive Cancer Center

type: Genome variation profiling by high throughput sequencing

summary: Through development of an in vivo orthotopic lung cancer model, we reveal an unanticipated pathway driving spontaneous metastasis that is orchestrated by the developmentally-regulated transcriptional repressor, Capicua (CIC).

overall_design: RNAseq and DNA copy number analysis of H1975 (EGFR-mutant lung adenocarcinoma) cells in the context of drug resistance to rociletinib


title: Small RNA-sequencing in apoptotic macrophages

status: Public on Oct 15 2015

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS


title: High-throughput small RNA sequencing of mouse primary macrophages treated with M-CSF withdrawal

summary: Analysis of small RNAs that are deregulated in apoptotic macrophages

overall_design: Sequencing of small-RNAs from  primary macrophages stimulated with M-CSF withdrawal

first: E

last: Repetto

first: M

last: Trabucchi

first: L

middle: E

last: Zaragosi

first: P

last: Barbry

first: K


title: Small molecule mediated annotation of miRNAs regulating HCV hijacking of lipid pathways

status: Public on Oct 19 2015

city: Ottawa

first: John

middle: Paul

last: Pezacki

state: ON

address: 150 Louis-Pasteur Pvt

department: Chemistry and Biomolecular Sciences

country: Canada

institute: University of Ottawa

summary: As part of SMART strategy, we aimed to characterize changes in miRNA expression associated with 25-hydroxycholesterol's antiviral effects.

overall_design: Huh7.5 hepatoma cells were infected with a cell culture adapted JFH1 strain (JFH-1T; MOI = 0.1).  48 hours post-infection, cells were treated with either 5 μM 25-hydroyxcholesterol or methanol (vehicle).  24 hours post- drug treatment, cells were lysed.

first: Ragunath

last: Singaravelu

middle: P


title: Comparison of the transcriptomic profile of intestinal epithelial cells (Caco-2 cells) treated with different PPARgamma agonists

status: Public on Oct 12 2015

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

institute: Lille University

summary: Peroxisome proliferator-activated receptor-gamma (PPARgamma) is a nuclear receptor highly expressed by colonic epithelial cells. It plays a key role in gut homeostasis and metabolism regulation. We previously showed that PPARgamma has a role in the action of aminosalycilates (5-ASA), one of the oldest anti-inflammatory agents used in the treatment of inflammatory bowel disease. These data have prompted us to develop novel analogues of 5-ASA with greater PPARgamma-activating properties (GED).  The various PPARgamma ligands appear to have some markedly different effects, some of which can induce adverse effects. The transcriptomic profiles induced by various families of PPARgamma ligands are very poorly known and especially in intestinal epithelial cells. Hence, the objectives of the present project is to compare the gene expression profile induced by GED, 5-ASA, and pioglitazone in Caco-2 cells, in order to better understand these compounds’ modes of action, to discover potential new PPARgamma target genes in intestinal epithelial cells and to explain the efficacy difference between GED and 5-ASA.

overall_design: 1 million of cells (plated in 6 wells plates) were treated with GED (1 mM for AGO samples and 30mM for GED samples), 5-ASA (30 mM), or pioglitazone (1  M) in DMEM without serum. When necessary, the vehicle DMSO (Sigma) was used as control (Ctrl). Serum deprivation was used 16 hours prior to stimulation in order to synchronize the cells. Experiment was done with 6 replicates for each treatment. After 24 hrs of stimulation, the wells were rinsed three times with sterile PBS at 4 C. Total RNA were extracted with the Nucleospin RNA kit (Macherey-Nagel, Hoerdt, France).

first: Mathurin

last: Fumery

first: Audrey

last: Langlois

first: Martin

last: Figeac

first: Pierre

last: Desreumaux

first: Benjamin

last: Bertin


title: Mytilus galloprovincialis, digestive gland and gill, exposed to Prorocentrum lima, producers of okadaic acid.

city: A Coruña

first: Juan

last: Fernandez Tajes

address: As Xubias

department: Genomics Area

institute: INIBIC

summary:
Differential expression analysis of digestive gland and gill tissues of mussels (Mytilus galloprovincialis) exposed to dinoflagellates (Prorocentrum lima), producers of okadaic acid, at a concentration of 200 cells/ml for one day.
Each sample consists in total RNA was extracted from pooled tissues of 5 individuals.

overall_design: Two-color dye-swap direct comparison experiment: exposed vs non-exposed (treated vs control). Biological replicates: two treated replicates and two control replicates per tissue.

last: Fernandez-Tajes


title: High-throughput small RNA sequencing of human primary macrophages stimulated with staurosporine

overall_design: Sequencing of small-RNA from human primary macrophages stimulated with an apoptotic stimuli


title: Transcription of mammalian cis-regulatory elements is restrained by actively enforced early termination

city: Vienna

first: Iros

last: Barozzi


title: Deep small RNA and degradome sequencing identifies new miRNAs-target pairs and novel PhasiRNAs in F-box regulatory networks in diploid strawberry

status: Public on Oct 06 2015

city: Guangzhou

first: Rui

last: Xia

state: Guangdong

address: 483 Wushan Rd, Tianhe

department: Horticulture

institute: South China Agricultural University

summary: The wild strawberry Fragaria vesca has recently emerged as an excellent model for investigating flower and fruit traits in economically important fruit crops. Its history of physiological studies combined with sequenced genome and full complements of molecular genetic tools facilitate investigations into mechanisms of its unique biological processes such as fleshy fruit development from the enlarged stem tip called receptacle. Sequencing of nine small RNA libraries encompassing vegetative, flower, and fruit tissues led to the identification of 22 conserved and 10 less-conserved miRNAs as well as 41 novel miRNAs that are likely specific to the strawberry. High throughput Parallel Analyses of RNA ends (PARE) were performed to identify miRNA-guided cleavage events and corresponding target genes. We found that most conserved miRNAs developed species-specific target genes in addition to conserved targets, highlighting the dynamic and fluid nature of the miRNA_target relations. Significantly, we discovered two novel clusters of miRNAs, which together target up to 94 F-box genes. Within one of the clusters is a 22 nt novel miRNA, miRN39, that was expressed preferentially in the developing receptacle fruit and triggered phased siRNA production from six primary FBX PHAS loci. This miRN39-phasiFBX pathway may be involved in regulating disease resistance in the receptacle fruit. In addition, a modified “two-hit” mode of tasiRNA processing was identified in F. vesca, suggesting flexibility in applying previously set rules. A major theme that emerges from this work is that novel miRNAs and miRNA-phasiRNA networks may have evolved to regulate recently expanded gene families so as to control species-specific biological or physiological processes.

overall_design: 8 sRNA libraries and 3 PARE (degradome) libraries without replicates

first: Songqing

last: Ye

first: Zongrang

last: Liu

first: Blake

last: Meyers

first: Zhongchi


title: ChIP-seq for Nanog in H9 hESC

status: Public on Oct 05 2015

city: Salt Lake City

first: Edward

last: Grow

state: UT

address: 2000 Circle of Hope Drive

department: Oncology

institute: University of Utah

summary: mapping Nanog TF binding sites in H9 hESC

overall_design: one sample of ChIP, one sample of input

first: Jens

last: Durruthy-Durruthy


title: Transcriptomic analysis of Blumeria graminis triticale on different hosts

status: Public on Nov 11 2015

city: Zurich

first: Fabrizio

last: Menardo

address: Zollikerstrasse 107

country: Switzerland

institute: University of Zurich

summary: With this experiment we aimed do identify eventual genes that are differentially expressed by the fungal pathogen Blumeria graminis triticale when it grows on two different hosts (wheat and triticale)

overall_design: We used to fungal isolates, for each of them we infected wheat and triticale and we extracted RNA (and sequenced) from the infected plant tissue. Three technical replicates for each combinations plant-pathogen were used

first: Beat

last: Keller


title: Gene expression analysis on ganglia derived from TH-MYCN mice

first: Daniel

last: Carter

summary: Amplification of the MYCN oncogene predicts treatment resistance in childhood neuroblastoma. Using a MYC target gene signature that predicts poor neuroblastoma prognosis we identified the histone chaperone, FAcilitates Chromatin Transcription (FACT), as a crucial mediator of the MYC signal and a therapeutic target in the disease. FACT and MYCN expression created a forward feedback loop in neuroblastoma cells that was essential for maintaining mutual high expression. FACT inhibition by the small molecule Curaxin compound, CBL0137, markedly reduced tumor initiation and progression in vivo. CBL0137 exhibited strong synergy with chemotherapy in standard use by blocking repair of DNA damage caused by genotoxic drugs, thus creating a synthetic lethal environment in MYCN amplified neuroblastoma cells and a treatment strategy for MYCN-driven neuroblastoma

overall_design: Superior Cervical ganglia and Coeliac ganglia were disected from Th-MYCN+/+ mice and wildtype age-matched littermates. RNA was isolated for hybridisation on Agilent arrays


title: Duchene Muscular Dystrophy Dogs Escapers and Affected Muscle Dogs Compared to Normal Dogs

city: Sao Paulo

first: Yuri

last: Moreira

state: Sao Paulo

address: Av. Prof. Lineu Prestes, 748 - Cidade Unersitária, São Paulo - SP, 05508-000, Brasil

department: Inst. Chemistry

country: Brazil

institute: USP

summary: Transcriptional profiling of dog muscle tissue comparing control dogs. tested, genomewide, for genes differentially expressed in muscle between the escapers and the affected dogs. Using Agilent mRNA SurePrint Canine arrays, we compared muscle gene expression of the two escapers, four affected, and four normal dogs at age 2 years.

overall_design: normal, affected DMD, and escapers

first: Y

first: N

last: Vieira


title: Expression data from liver samples overxpressing either the GFP or ChREBP

status: Public on Oct 01 2015

city: Pars

first: Renaud

last: Dentin

address: 24 rue du Faubourg Saint Jacques

department: Endocrinology, Metabolism and Diabetes

institute: INSERM U1016

summary:
The GFP or ChREBP were overexpressed in the liver of C57Bl6/J mice through adenoviral gene delivery. Mice were studied in the fed state 3 weeks later.
We used microarray analysis to detail the global programme of gene expression underlying ChREBP overexpression and identified distinct classes of up and down regulated genes.

overall_design: RNA extraction and hybridization on Affymetrix microarrays.

first: Julien

last: Bricambert


title: Expression data from liver samples overxpressing either the GFP or Phf2

summary:
The GFP or Phf2 were overexpressed in the liver of C57Bl6/J mice through adenoviral gene delivery. Mice were studied in the fed state 3 weeks later.
We used microarray analysis to detail the global programme of gene expression underlying Phf2 overexpression and identified distinct classes of up and down regulated genes.


title: Detection and Characterization of Gene Expression Differences in Transgenic Glycine max Seeds with RNAseq

status: Public on Oct 04 2015

city: Charlotte

first: Kevin

middle: Chad

last: Lambirth

address: 9201 University City Blvd

department: Biological Sciences

institute: University of North Carolina at Charlotte

summary: Transformation of Glycine max with seed-targeted expression vectors via Agrobacterium causes measurable unscripted gene expression changes in the seed transcriptome

overall_design: mRNA was sequenced from three transgenic events expressing three different recombinant proteins in soybean seeds.  Three plants were chosen from each as group replicates, and three seeds from each plant as individual biological replicates.

first: Kenneth

last: Bost


title: High-frequency generation of fertile transgenic mice from H19-Igf2 engineered androgenetic haploid embryonic stem cells

status: Public on Nov 05 2015

city: Beijing

first: Meili

last: Zhang

address: Dong Dan San Tiao 5

department: State Key Laboratory of Medical Molecular Biology, Department of Medical Genetics

institute: Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College

type: Genome variation profiling by genome tiling array

summary: Recent success in the derivation of mouse haploid embryonic stem cells from androgenetic blastocysts (ahESCs) has provided new avenues for the generation of genetically modified animals. However, the efficiency to produce viable transgenic mice via intracytoplasmic ahESCs injection (ICAI) was very low, which may correlate with the aberrant regulation of imprinted genes. Here we designed to delete the paternal imprinted gene H19 by CRSPR-Cas9 system combined with homologous recombination. The H19 deleted (H19Δ) ahESCs maintained haploidy and genome integrity, expressed pluripotency markers, differentiated into embryoid bodies (EBs), and contributed to chimeras after blastocyst injection. These cells exhibited similar imprinting features with sperm cells, and can produce fertile progenies after ICAI at a high efficiency. More importantly, it is feasible to perform genetic manipulations in H19Δ ahESCs, and the genomic modifications can be properly transmitted to offspring. Our study will benefit the reproductive medicine in curing the hereditary genetic diseases and infertility in the future.

overall_design: The copy number variations of the two H19Δ ahESC lines were analyzed by the SurePrint G3 Mouse CGH 4×180 K microarrays (Agilent).  Wild-type OG-3 ahESCs were used as reference.

first: Yue

last: Huang


title: Genetic and Acquired Lysosomal Disorders Drive Susceptibility to Tuberculosis by Compromising Macrophage Migration

status: Public on Oct 21 2015

city: Seattle

first: Russell

last: Berg

state: WA

institute: University of Washington

summary: A zebrafish forward genetic screen for determinants of susceptibility to Mycobacterium marinum identified a hypersusceptible mutant deficient in the lysosomal hydrolase Cathepsin L that manifests the hallmarks of human lysosomal storage diseases. In uninfected mutants, macrophages progressively accumulate undigested material in their lysosomes, leading to impaired migration and the accumulation of unengulfed cell debris. During mycobacterial infection, these vacuolated macrophages cannot migrate to phagocytose infected macrophages undergoing apoptosis in the tuberculous granuloma. Consequently, unengulfed apoptotic macrophages undergo secondary necrosis causing granuloma breakdown and increased mycobacterial growth. Macrophage lysosomal accumulations similarly impair migration to newly infecting mycobacteria. We find that important aspects of this phenotype are recapitulated in human smokers, who are at increased risk for tuberculosis. A majority of alveolar macrophages from smokers exhibit lysosomal accumulations and do not migrate to Mycobacterium tuberculosis. This incapacitation of highly microbicidal first-responding macrophages may contribute to smokers' susceptibility to tuberculosis.

overall_design: A forward genetic screen for zebrafish larvae that are hypersusceptible to Mycobacterium marinum infection identified a mutation in the transcription factor snapc1b at 13: 37996163 (T->C). Individuals of wild type (T/T) and mutant (C/C) were genotyped and pooled respectively for RNA isolation and transcriptome analysis.

first: Steven

last: Levitte

first: Seonadh

last: O'Leary

first: Mary

last: O'Sullivan

first: C

last: Cambier

first: James

last: Cameron

last: Takaki

first: Joseph

last: Keane

first: David

last: Tobin

first: Lalita

last: Ramakrishnan


title: Islet mRNA changes in rat pancreatic islets during aging

status: Public on Sep 30 2015

city: Lausanne

first: Romano

last: Regazzi

address: Rue du Bugnon 9

department: DNF

institute: University of Lausanne

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

summary:
comparison of mRNA expression in the islets of 3- and 12-month old male Wistar rats
Aging is a risk factor for a majority of metabolic diseases including type 2 diabetes. During aging pancreatic beta-cell function decreases leading to impaired insulin secretion and proliferation and to an increase in apoptosis. Impairment of pancreatic beta cell functions and survival has been linked to gene expression changes. The aim of our study was to obtain a global expression profile of microRNAs and mRNAs of pancreatic islets of 3 and 12 month old male Wistar rats in order to identify the changes occurring during aging.

overall_design: RNA was isolated from pancreatic islets of three 3-month old and three 12-month old rats and was further analyzed by microarray

first: Ksenia

last: Tugay


title: Islet microRNA changes in the rat pancreatic islets during aging

summary:
comparison of microRNA expression in the islets of 3- and 12-months old male Wistar rats
Aging is a risk factor for a majority of metabolic diseases including type 2 diabetes. During aging pancreatic beta-cell function decreases leading to impaired insulin secretion and proliferation and to an increase in apoptosis. Impairment of pancreatic beta cell functions and survival has been linked to gene expression changes. The aim of our study was to obtain a global expression profile of microRNAs and mRNAs of pancreatic islets of 3 and 12 month old male Wistar rats in order to identify the changes occurring during aging.

overall_design: Total RNA isolated from the pancreatic islets of three 3-month old and four 12-month old rats was analyzed by microarray to determine the microRNA profile


title: microRNA and mRNA expression in pancreatic islets of 3 and 12 month old male Wistar rats

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

overall_design: Refer to individual Series


title: RNA-Sequencing analysis of the Drosophila transcriptomic response to infection by entomopathogenic nematodes and their mutualistic bacteria

status: Public on Sep 12 2015

first: Priti

last: Kumari

address: 801 W Baltimore St

department: Institute For Genome Sciences

institute: University Of Maryland Baltimore School Of Medicine

summary: We report the application of next generation RNA sequencing to analyze the transcriptional response of Drosophila adult flies to infection by the insect pathogenic nematodes Heterorhabditis bacteriophora and their mutualistic bacteria Photorhabdus luminescens, either separately or together. We find that Heterorhabditis and Photorhabdus differentially modulate a large number of genes, many of which participate in metabolic functions, stress responses, repression of gene transcription and neuronal activities. We have also identified Drosophila genes with potential role in nematode recognition and others with putative anti-nematode properties. These findings generate novel insights into how the host immune function is shaped to respond against nematode parasites and their associated bacteria.

overall_design: Transcriptional profiles of Drosophila wild-type adult flies infected with Heterorhabditis bacteriophora carrying or lacking Photorhabdus or the bacteria alone were generated at 12 and 30 hours post infection using Illumina deep sequencing technology.

first: Ioannis

last: Eleftherianos

first: Julio

middle: C

last: Castillo


title: Expression data from pooled biological replicates (n=6) from MEF2D knockdown in neonatal rat ventricular myocytes (NRVMs)

status: Public on Aug 31 2015

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary:
Differentiation and maintenance of cardiac muscle is a complex biological process. MEF2D appears to play an important role in the regulation of cardiomyocyte homeostasis.
We knocked down expression of MEF2D in NRVMs, and assessed global expression pattern changes in MEF2D knockdown against a negative control.

overall_design: NRVMs were extracted from 1 to 2 day old rat pups and were allowed to recover for 24 hours before being transduced with shRNA viral vectors to knockdown expression of MEF2D or LacZ (negative control). After 3 days, total RNA was harvested for Affymetrix global gene expression microarray analysis. Each array was pooled RNA from six biological replicates.

first: Nelsa

last: Estrella

first: Amanda

last: Clark

first: Cody

last: Desjardins

first: Sarah

last: Nocco

first: Francisco

middle: J

last: Naya


title: Human pluripotent stem cell-derived neural constructs for predictive neurotoxicity screening

status: Public on Sep 08 2015

city: Cleveland

first: Peng

last: Jiang

state: OH

address: 2121 Euclid Ave

institute: Cleveland State University

summary: Human pluripotent stem cell-based in vitro models that reflect human physiology have the potential to reduce the number of drug failures in clinical trials, and offer a cost effective approach for assessing chemical safety.  Here, human embryonic stem (ES) cell-derived neural progenitor cells, endothelial cells, mesenchymal stem cells, and microglia/macrophage precursors were combined on chemically-defined poly(ethylene glycol) (PEG) hydrogels and cultured in serum-free media to model cellular interactions of the developing brain.  The precursors self-assembled into 3-dimensional (3D) neural constructs with cortically organized neuronal and glial cells, interconnected vascular networks, and ramified microglia. Replicate constructs were highly reproducible by RNA sequencing (Spearman’s correlation coefficients, ρ ≥ 0.97) and robustly expressed neurogenesis, vasculature development, and microglia genes.  Finally, linear support vector machines were used to construct a predictive model from RNA sequencing data for 240 neural constructs treated with 60 toxic and non-toxic chemicals, which then correctly classified 9/10 blinded compounds.

overall_design: Note that all cell types were derived from the H1 human embryonic stem cell line. 11 samples for initial quality control (triplicate day 13 neural progenitor cells; quadruplicate day 21 neural progenitor cells cocultured with mesenchymal stem cells and endothelial cells; quadruplicate day 21 neural progenitor cells cocultured with mesenchymal stem cells and endothelial cells and migroglia/macrophage precursor cells), quadruplicate samples of H1 ES cells as a control for comparing to untreated toxicity study samples, and 288 samples associated with toxicity screening (all samples formed using neural progenitor cells, endothelial cells, mesenchymal stem cells, and microglia/macrophage precursors).

first: Michael

last: Schwartz

first: Zhonggang

last: Hou

first: Nicholas

last: Propson

first: Jue

last: Zhang

first: Vitor

last: Costa

first: Bao

middle: K

last: Nguyen

first: Jennifer

middle: M

last: Bolin

first: Collin

last: Engstrom

first: William

last: Daly

first: Yu

last: Wang

first: Ron

last: Stewart

last: Page

middle: L

last: Murphy

last: Thomson


title: Expression data from CEA high and CEA low cells in colorectal cancer

status: Public on Aug 27 2015

city: Wuhan

first: Chang

last: Yan

state: Hubei

address: Jiefang Road

department: Gastrointestinal Surgery

institute: Tongji Hospital

summary: We used microarrays to detailed global expression of colorectal cancer cells that expressed high or low levels of carcinoembryonic antigen.

overall_design: CEA high and CEA low cells were purified from LoVo and xenograft tumor derived from colorectal cancer patient (xhCRC) and were used for RNA extraction.

first: Yan

last: Chang


title: Stationary phase stimulon and CspC regulon

status: Public on Aug 24 2015

city: São Paulo

first: Juliana

middle: da Silva

last: Santos

state: SP

address: Avenida Professor Lineu Prestes, 1374

department: Microbiology

institute: Institute of Biomedical Sciences from University of São Paulo

summary: The cold shock proteins belong to a family of RNA binding proteins presenting a highly conserved domain, called cold shock domain (CSD). They are involved in various cellular processes, including adaptation to low temperature, nutritional stress, cell growth and stationary phase. Here we investigate the role of CspC in C. crescentus stationary phase and the molecular mechanisms underlying gene regulation by this protein. A global transcriptional profiling experiment comparing cspC and the wild type strain both at exponential and stationary phases was carried out. The results showed that the absence of cspC affected the transcription of 20 genes at exponential phase and 65 genes at stationary phase. Genes encoding enzymes of the glyoxylate cycle were severely downregulated in the mutant at stationary phase. The stationary phase-induced RNA binding protein CspC has an important role in gene expression at this phase. It is required for the expression of the essential gene sciP, the ECF sigma factor sigU, as well as of the genes for the glyoxylate cycle enzymes and for oxidative stress response.

overall_design: Two and three replicates were performed to determine the stationary phase stimulon and CspC regulon, respectively. Each replicate was conducted with an independent biological sample.

first: J

first: C

last: da Silva

first: H

last: Balhesteros

first: R

middle: F

last: Lourenço

first: M

middle: V

last: Marques


title: Transcriptome analyses of skeletal muscle in αB-crystallin/HspB2 knockout and wild-type mice on a normal or high fat diet

status: Public on Sep 01 2015

city: Chicago

first: Daniel

last: Toft

address: 675 N. St. Clair Street, 14-100

department: Endocrinology

institute: Northwestern University

summary: We profiled the skeletal muscle transcriptome between wild type and αB-crystallin/HspB2 knock mice exposed to normal chow and high fat diets to examine the role of αB-crystallin/HspB2 in diet induced obesity.   Combined with metabolic profiling of the mice, these data reveal that αB-crystallin/HspB2 is involved in the genesis of insulin resistance on a high fat diet, and we provide extensive RNA profiling to illuminate potential mechanistic insights into the muscle-specific role of αB-crystallin/HspB2.

overall_design: Hind limb muscle mRNA profiles of wild type and αB-crystallin/HspB2 knock mice exposed to either normal chow or high fat diets using RNAseq analysis

first: Brian

middle: T

last: Layden


title: Med1 Deletion in Heart Causes Dilated Cardiomyopathy

status: Public on Aug 15 2015

first: Navin

last: Viswakarma

address: 303 E Chicago Ave

department: Pathology

summary: Global gene expression analysis reveals that Med1 regulates many genes involved in energy metabolism, calcium signaling, and oxidative phosphorylation in myocardium.

overall_design: RNA samples were prepared from hearts of 5 controls Med1 floxed mice (Med1fl/fl) and 5 Cre-loxP-mediated cardiomyocyte-specific deletion of Med1 (csMed1-/-) mice. RNA were pooled and subjected to RNA-seq analysis.

first: Yuzhi

last: Jia

first: Hsiang-Chun

first: Matthew

last: Schipma

first: Yi-Jun

last: Zhu

first: Bayar

last: Thimmapaya

first: Janardan

last: Reddy


title: Whole genome transcritptional comparison of Group A Streptococcus (Streptococcus pyogenes) serotype M1 pre-epidemic and epidemic isolates

status: Public on Aug 10 2015

city: Houston

first: Stephen

middle: B.

last: Beres

state: TX

address: 6670 Bertner Ave.

department: Pathology and Genomic Medicine

institute: Houston Methodist Research Institute

summary: This transcriptional analysis is a follow up to a population genomic investigation of 3615 Streptococcus pyogenes serotype M1 strains whch are responsible for an epidemic of human invasive infections (www.pnas.org/cgi/doi/10.1073/pnas.1403138111), The goal was to assess gene expression differences between predecessor pre-epidemic M1 strains and their descendent epidemic M1 strains to gain insights into the underlying genetic basis for the shift in the frequency and severity of human infections caused by these pathogenic bacteria

overall_design: The transcriptomes of 7 GAS M1 strains, 4 pre-epidemic and 3 epidemic, were compared at two phases of growth, mid-exponential and early-stationary, using 3 biologial replicates, to identify genes differentially expressed between the pre-epidemic and epidemic isolates with the goal of to gaining insight into the underlying genetic basis for the evolutionary emergence, increased frequency and severity of the epidemic strains relative to the pre-epidemic strains

first: James

last: Musser

middle: B


title: mRNA profiling of hypoxia+SU5416-induced pulmonary hypertension (PH) mouse model treated with an inhibitor of miR-130/301 family

status: Public on Sep 29 2015

first: Thomas

last: BERTERO

address: 77 Av Louis Pasteur

department: Cardiology

institute: Brigham and women hospital, Harvard Medical School

summary:
Purpose: Guided by an in silico combination of microRNA (miRNA) target prediction, analysis of transcriptomic changes in 137 human diseases, and advanced gene network modeling, we predicted the miR-130/301 family of miRNAs as a shared regulator of a fibrotic gene network across human diseases, thus orchestrating broad control over disease manifestation. The goals of this study are to compare the lung mRNA profile of mouse model of Pulmonary hypertension, one of the most fibrotic pathology uncovered by our in silico prediction, treated with an inhibitor of miR-130/301 (Short-130) to mice treated with a control inhibitor (Short-NC).
Methods: Eight-week-old mice (C57BL/6) were injected with SU5416 (20 mg/kg/dose; Sigma-Aldrich), followed by exposure to normobaric hypoxia (10% O2; OxyCycler chamber, Biospherix Ltd.) for 2 weeks. After 2 weeks and confirmation of PH development in 5 mice (right heart catheterization), mice were further treated with 3 intrapharyngeal injections (every 4 days) of control or miR-130/301 shortmer oligonucleotides, designed as fully modified antisense oligonucleotides complementary to the seed sequence of the miR-130/301 miRNA family (10 mg/kg/dose; Regulus). Specifically, the control and miR-130/301 shortmer oligonucleotides were nontoxic, lipid-permeable, high-affinity oligonucleotides. The miR-130/301 shortmer carried a sequence complementary to the active site of the miR-130/301 miRNA family, containing a phosphorothioate backbone and modifications (fluoro-, methoxyethyl, and bicyclic sugar) at the sugar 2’ position. Three days after the last injection, right heart catheterization was performed followed by harvesting of lung tissue for RNA extraction. Lung mRNA profiles of those mice or control mice (Normoxia+SU5416) were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000. The sequence reads that passed quality filters were analyzed at the gene-level count. The gene level counts were then normalized with the R/Bioconductor package limma using the voom /variance stabilization method. The data were quality controlled for outliers using principal component analysis (PCA). Differential expression analysis between transcriptome profiles of experimental groups was performed using the R / Bioconductor package limma.
Results: Transcriptomic analyses of whole lung from mice with hypoxia+SU5416-induced PH revealed a generalized de-repression of miR-130/301 targets by Short-130 treatment. Importantly, although whole lung transcriptomics likely captured only a subset of the miR-130/301 targets affecting the diseased pulmonary vasculature, pathway enrichment nonetheless revealed pronounced representation of several pathways known to be involved in fibrosis. Thus, the miR-130/301 family indeed induces a programmatic shift at the molecular level toward the fibrotic pathophenotype in vivo

overall_design: Whole lung mRNA profiles of Normoxia (Control) and hypoxia+SU5416-induced PH mice treated with Short-NC or Short-130 were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000.

last: Bertero

first: Vivek

last: Kaimal

first: Nelson

last: Chau

middle: Y

last: Chan