title: Changes in relative transcript amounts caused by ∆pbp1a, double ∆pbp1a mltG(∆488bp), and triple ∆pbp1a mltG(∆488bp) ∆pbp2b mutations in Streptococcus pneumoniae

status: Public on Apr 19 2016

city: Bloomington

first: Malcolm

middle: E

last: Winkler

state: IN

address: 1001 E. Third Street

department: Biology

institute: Indiana University

summary: In ellipsoid-shaped ovococcus bacteria, such as the respiratory pathogen Streptococcus pneumoniae (pneumococcus), side-wall (peripheral) peptidoglycan (PG) synthesis emanates from midcells and is catalyzed by the essential class B penicillin-binding protein PBP2b transpeptidase (TP). We report that mutations that inactivate the pneumococcal YceG-domain protein, Spd_1346 (renamed MltG), remove the requirement for PBP2b. ΔmltG mutants in unencapsulated strains accumulate inactivation mutations of class A PBP1a, which possesses TP and transglycosylase (TG) activities. To gain insight into the mechanism of synthetic-viable genetic relationships involving Δpbp1a, we performed RNA-Seq analyses of Δpbp1a, Δpbp1a mltG(Δ488bp), and Δpbp1a mltG(Δ488bp) Δpbp2b mutants compared to the isogenic unencapsulated parent strain. Unexpectedly, the Δpbp1a deletion causes an almost exclusive induction in relative transcript amounts of genes that are in the WalRK TCS regulon, which includes established and putative PG hydrolases and division proteins of unknown functions.

overall_design: RNA was prepared from cultures of strains IU6741 (∆pbp1a), IU8553 (∆pbp1a mltG(∆488bp)), IU8567 (∆pbp1a mltG(∆488bp) ∆pbp2b) and IU1824 (pbp1a+ mltG+ pbp2b+ parent) grown exponentially in BHI media at 37ºC to OD620 ≈0.15 to 0.2. Three independent biological replicates of RNA were prepared for each strain or condition. cDNA libraries were sequenced and the sequencing results were used as the data base for differential expression analysis.

first: Ho-Ching

last: Tsui

first: Kurt

last: Zimmer

first: Douglas

last: Rusch

first: Kevin

last: Bruce


title: Expression data from GRMD skeletal and cardiac muscles

status: Public on Apr 29 2016

city: Pittsburgh

first: Cristi

middle: Lara

last: Galindo

state: Pennsylvania

address: 200 Lothrop Avenue

country: USA

institute: University of Pittsburgh

summary:
Duchenne muscular dystrophy (DMD) is an X-linked genetic disease that affects 1 in 5,000 males. Skeletal muscle wasting occurs early in childhood, while cardiac involvement does not typically surface until a decade later. There is currently no method for predicting which patients will develop cardiomyopathy.  The molecular reasons for the differences in timing and progression of cardiac dysfunction compared to skeletal dysfunction are unknown.
We used miscroarrays to compare the two tissue types at different ages of disease progression.

overall_design: All dogs were used and cared for according to principles outlined in the National Research Council Guide for the Care and Use of Laboratory Animals.  Dogs were housed at the University of North Carolina at Chapel Hill.  Affected dogs were identified based on dramatic elevation of serum creatine kinase (CK) and genotyped for confirmation. A total of 15 animals were included in the study: 3 young GRMD dogs (6-7.5 months), 3 older GRMD dogs (12-13 months), 6 age-matched wild type control animals, and 3 GRMD dogs of advanced age (47, 52, and 93 months-old). From a physiologic standpoint, the first year of a golden retriever’s life is analogous to the first 20 years of a human’s [21]. Thus, by dividing these ages into quartiles, 6 and 12 golden retriever months would equate to 10 and 20 human years.  The natural disease course of GRMD tends to parallel DMD up to 6 months, with an onset of debilitating weakness and postural changes in both conditions.  With this said, dogs with GRMD typically do not have overt clinical cardiac disease until 2 years of age or considerably later [20], well beyond their onset of skeletal muscle involvement and consistent with the relative delayed onset of cardiomyopathy in human DMD. The medial head of the gastrocnemius (MHG) and left ventricular (LV) free wall [17, 22] tissue samples were removed at necropsy, snap frozen in a Freon substitute, cooled in liquid nitrogen, stored at -80o C, and shipped in cryovials to Vanderbilt for analysis.  Serum samples collected by venipuncture near the time of necropsy (either 6 or 12 months) and an earlier time point (generally 4-6 weeks), stored in cryovials at -80o C,  were also shipped to Vanderbilt.

middle: L

first: Larry

middle: W

last: Markham


title: Transcriptome of Vibrio fischeri ES114 in rich medium, seawater, and after venting from the Hawaiian bobtail squid Euprymna scolopes

status: Public on Apr 26 2016

city: La Jolla

first: Luke

last: Thompson

state: CA

address: 9500 Gilman Dr

institute: UC San Diego

type: Expression profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

summary: We report the full transcriptome (RNA-Seq) of Vibrio fischeri ES114 in rich medium, seawater, and after venting from the Hawaiian bobtail squid Euprymna scolopes. We also report the effects of ribodepletion on low-biomass samples, down to input amount of 1ng total RNA.

overall_design: We performed RNAseq experiments on V. fischeri cells in culture, cells that were incubated in artificial seawater, and cells collected during expulsion from the squid host in order to look for transcriptional signals that were directly associated with host colonization.

middle: R

first: Kiel

last: Nikolakakis


title: Transcriptomic Analysis of Staphylococcal sRNAs: Insights into Species Specific Adaption and the Evolution of Pathogenesis

status: Public on Apr 25 2016

city: Tampa

first: Andy

last: Weiss

state: Florida

address: 4202 East Fowler Avenue, ISA2015

department: Department of Cell Biology, Microbiology and Molecular Biology

institute: University of South Florida

summary: Next-generation sequencing technologies have dramatically increased the rate at which new genomes are sequenced. Accordingly, automated-annotation programs have become adept at identifying and annotating protein coding regions, as well as common and conserved RNAs. Additionally, RNAseq techniques have advanced our ability to identify and annotate regulatory RNAs (sRNAs), which remain significantly understudied. Recently, our group catalogued and annotated all previously known and newly identified sRNAs in several Staphylococcus aureus strains. These complete annotation files now serve as tools to compare the sRNA content of S. aureus to other bacterial strains to investigate the conservation of their sRNomes. Accordingly, in this study we performed RNAseq on two staphylococcal species, S. epidermidis and S. carnosus, identifying 118 and 89 sRNAs in these organisms, respectively. The sRNA content of all three species were then compared to elucidate their common and species-specific sRNA content, identifying a core set between 53 and 36 sRNAs encoded in each organism. In addition, we determined that S. aureus has the largest set of unique sRNAs (137) while S. epidermidis has the fewest (25). Finally, we identify a highly conserved sequence and structural motif differentially represented within, yet common to, both S. aureus and S. epidermidis. Collectively, in this study, we uncover the sRNome common to three staphylococcal species, shedding light on sRNAs that are likely to be involved in basic physiological processes common to the genus. More significantly, we have identified species-specific sRNAs that are likely to influence the individual lifestyle and behavior of these diverse staphylococcal strains.

sample_organism:
Staphylococcus aureus
Staphylococcus carnosus
Staphylococcus epidermidis

overall_design: Three RNAseq data sets in total.  Each sample was generated by pooling three independent biological replicate RNA preps

first: William

middle: H

last: Broach

first: Lindsey

middle: N

last: Shaw


title: microRNA Expression profiles of parental Panc1 cell lines and Gemcitabine resistance Panc1 cell lines

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

summary: Gemcitabine (GEM) is a key drug for treating PDAC, and it is commonly used for adjuvant chemotherapy. Although the majority of PDAC is sensitive to GEM at first, GEM cannot control PDAC for very long, suggesting that PDAC develops resistance to GEM after prolonged exposure. No reliable predictors of susceptibility to gemcitabine chemotherapy exist in pancreatic ductal adenocarcinoma. MicroRNAs (miR) are epigenetic gene regulators with tumorsuppressive or oncogenic roles in various carcinomas. This study assesses gemcitabine resistant PDAC for its specific miR expression pattern. Gemcitabine resistant variants of Panc1, a human pancreatic adenocarcinoma cell line, were established. MicroRNA screening was investigated by microarray.

overall_design: GEM-resistant cells were generated by exposure to gradually increasing concentrations of the reagent for 2 months. Parental Panc1cells (Panc1-Pt) were exposed to GEM at an initial concentration of 2 ng/ml. When the cells adapted, the GEM concentration was increased. The final GEM concentration was 30 ng/ml. Limiting the dilution of the established cells allowed the cloning of the GEM-resistant Panc1cells, and the three independent clones (Panc1-GRs: Panc1-GR1, -GR3, and –GR4) were used in the present experiments. Extracted total RNA was labeled with Hy5 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark). Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc.. The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’signal intensities of 95% confidence intervals. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. A relative expression level of a given miRNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments. 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

first: S

last: Hasegawa

first: Mi

last: Mikamori

first: H

last: Eguchi


title: Analysis of gene expression during the early stages of zebrafish heart valve development

status: Public on Apr 15 2016

city: Illkirch

first: Julien

last: Vermot

address: 1 rue Laurent Fries

country: France

institute: IGBMC

summary: We report changes in the levels of gene expression between 48hpf hearts and 56hpf hearts, the initial stages of valvulogenesis

overall_design: 48hpf and 56hpf hearts were dissected and RNA was extracted. RNA profiles were then generated at each stage using Illumina deep sequencing

first: Emily

last: Steed


title: Chronic Intermittent Ethanol by vapor chamber gene expression time-course in nucleus accumbens [NAC]

city: Richmond

first: Michael

last: Miles

state: VA

department: Pharmacology and Toxicology

institute: Virginia Commonwealth Univ.

summary:
Lasting behavioral and physiological changes such as abusive consumption, dependence, and withdrawal are characteristic features of alcohol use disorders (AUD). Mechanistically, persistent changes in gene expression are hypothesized to contribute to these brain adaptations leading to ethanol toxicity and abuse. Here we employed repeated chronic intermittent ethanol (CIE) exposure by vapor chamber as a mouse model to simulate the cycles of ethanol exposure and withdrawal commonly seen with AUD. This model has previously been shown to induce progressive ethanol consumption in rodents. Brain regional expression networks contributing to CIE-induced behavioral changes were identified by microarray analysis across five brain regions in the mesolimbic dopamine system and extended amygdala with tissue harvested from 0-120 hours following the last cycle of CIE. Weighted Gene Correlated Network Analysis (WGCNA) was used to identify gene networks over-represented for CIE-induced temporal expression changes across brain regions. Differential gene expression analysis of CIE vs. air-treated controls showed that long-lasting gene regulation occurred 5-days after the final cycle of ethanol exposure only in prefrontal cortex (PFC) and hippocampus. In the majority of brain-regions, however, ethanol regulated gene expression changes occurred only immediately following CIE or within the first 8-hours of removal from ethanol.
Bioinformatics analysis of modules identified by WGCNA showed that neuroinflammatory responses were seen across multiple brain regions at early time-points, whereas co-expression modules related to neuroplasticity, chromatin remodeling, and neurodevelopment were seen at later time-points and in specific brain regions (PFC or HPC). In PFC a module containing Bdnf was identified as highly CIE responsive in a biphasic manner, with peak changes at 0 hours and 5 days following CIE, suggesting a possible role in mechanisms underlying long-term molecular and behavioral response to CIE. Strikingly, bioinformatics analysis of this network and several other modules identified Let-7 family microRNAs as potential regulators of gene expression changes induced by CIE. Our results suggest a complex temporal and regional pattern of widespread gene network responses involving neuroinflammatory and neuroplasticity related genes as contributing to physiological and behavioral responses to chronic ethanol. In particular, our identification of a potential role for Let-7 miRNAs and a Bdnf-related expression network in long-lasting expression changes after CIE may lead to future druggable gene target identification for novel intervention in AUD.

overall_design: Adult male C57BL/6J mice (n=48) received either ethanol vapor exposure (CIE) in plexiglass inhalation chambers, or only air exposure in the inhalation chambers (Ctrl). Ethanol vapor concentrations were monitored daily and air flow was adjusted to maintain ethanol concentrations within a range (10-13 mg/l air). Before each chronic ethanol exposure cycle, intoxication was initiated in the CIE group by administration of ethanol (1.6 g/kg), and blood ethanol concentration was stabilized by injection of the alcohol dehydrogenase inhibitor pyrazole (1 mmol/kg).  Both ethanol and pyrazole were administered intraperitoneally (i.p.) in a volume of 0.02 ml/g body weight.  Ctrl mice were handled similarly, but administered saline and pyrazole (i.p.) prior to being placed in air only chambers. Mice spent 4 days in the inhalation chamber for 16hr/day. Following 4 days in the inhalation chamber mice underwent 7 days of complete abstinence from ethanol. At the end of the abstinence period, mice were returned to the inhalation chamber to begin the next cycle of CIE. This pattern of 4 days CIE (or air) exposure followed by 7 days abstinence was repeated for four complete cycles. Immediately following the last cycle of air or ethanol exposure as above, mice were removed from the inhalation chambers and euthanized at the appropriate time point by decapitation. Time points collected were 0, 8, and 72 hours (h) and 7 days (d), with n=6 for each treatment/time group. Gene expression was quantified with Affymetrix GeneChip Mouse Genome 430 2.0 arrays. Scanning data was stored in CEL file format using Affymetrix Expression Console software. Microarray data was analyzed using RMA normalization; ComBat to minimize batch effects; linear models for microarrays (LIMMA) to determine differences in gene expression between CIE and Ctrl groups; and Weighted Gene Correlated Network Analysis (WGCNA) to identify modules of co-expressed genes representing specific biological pathways. Modules were overlapped with genes differentially expressed between CIE and Ctrl mice at each time-point to identify modules regulated at specific times after CIE. Open source bioinformatics resources were further used to determine biological pathways represented by WGCNA modules.

middle: F

first: Howard

middle: C

last: Becker

first: Maren

last: Smith


title: Chronic Intermittent Ethanol by vapor chamber gene expression time-course in basal nucleus of the stria terminalis [BNST]


title: Chronic Intermittent Ethanol by vapor chamber gene expression time-course in central nucleus of amygdala [CEA]


title: Expression analysis of M. tb H37Rv after treatment with DTT for 3 hrs

status: Public on Apr 14 2016

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

summary: Effect of Thiol reductive stress (DTT 5mM) on M.tb Rv was studied.

overall_design: DTT reduced at 5 mM concentration was added to log pahse culture of M.tb H37Rv. After 3 hours RNA was isolated and  hybridization was done on  Affym Affymetrix microarrays.

first: A

last: Trivedi

first: P

middle: S

last: Mavi

first: D

last: Bhatt

last: Kumar


title: Real-time quantitative PCR analysis of S100A8 and S100A9 effects on lung

status: Public on Aug 01 2016

city: UNSW, SYDNEY

first: Kenneth

middle: K

last: Hsu

state: NSW

address: Rm422, 4E, Wallace Wurth Bld,

department: School of Medical Sciences

country: Australia

institute: University of New South Wales

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

overall_design: Refer to individual Series


title: Ctf4 links DNA replication with sister chromatid cohesion establishment by recruiting the Chl1 helicase to the replisome

status: Public on Apr 08 2016

city: London

first: Catarina

last: Samora

address: 44 Lincoln's Inn Fields

country: United Kingdom

institute: The Francis Crick Institute

type: Genome binding/occupancy profiling by genome tiling array

summary: DNA replication during S-phase is accompanied by establishment of sister chromatid cohesion to ensure faithful chromosome segregation. The Eco1 acetyltransferase, helped by factors including Ctf4 and Chl1, concomitantly acetylates the chromosomal cohesin complex to stabilize its cohesive links. Here we show that Ctf4 recruits the Chl1 helicase to the replisome via a conserved interaction motif that Chl1 shares with GINS and polymerase α. We visualize recruitment by EM analysis of a reconstituted Chl1-Ctf4-GINS assembly. The Chl1 helicase facilitates replication fork progression under conditions of nucleotide depletion, however this function does not require Ctf4 interaction. Conversely, Ctf4 interaction, but not helicase activity, is required for Chl1’s role in sister chromatid cohesion. A physical interaction between Chl1 and the cohesin complex during S-phase suggests that Chl1 contacts cohesin to facilitate its acetylation. Our results reveal how Ctf4 forms a replisomal interaction hub that coordinates replication fork progression and sister chromatid cohesion establishment.

overall_design: The Affymetrix Saccharomyces cerevisiae Chip Tiling 1.0R Arrays were used to analyze the incorporation of BrdU and the localization of Chl1 and Ctf4 in Saccharomyces cerevisiae in S-phase arrested cells.

middle: P

first: Julie

last: Saksouk

first: Panchali

last: Goswami

first: Ben

middle: O

last: Wade

first: Martin

last: Singleton

first: Paul

middle: A

last: Bates

first: Armelle

last: Lengronne

first: Alessandro

last: Costa

first: Frank

last: Uhlmann


title: Chronic Intermittent Ethanol by vapor chamber gene expression time-course in medial prefrontal cortex [PFC]

first: Michael

last: Miles

last: Becker


title: RNA-Sequencing of Klf6 silenced oligodendrocytes

status: Public on Apr 01 2016

city: New York

first: Gareth

last: John

state: New York

address: 1 Gustave Levy Place

department: Neurology

institute: Icahn School of Medicine at Mount Sinai

summary: We examine the role of Klf6 in oligodendrocyte progenitor cells and determine that Klf6 acts as a gp130-sensitive transactivator of the nuclear import factor importin-α5 (Impα5), a key controller of nuclear trafficking in oligodendrocytes.

overall_design: Examination of expression profiles of 2 different cell stages exposed to siRNA vs. control

first: Benjamin

last: Laitman


title: An integrated approach combining RNA-seq, Ribo-seq and Proteomics identifies the coding potential of Mycobacterium abscessus

status: Public on Mar 30 2016

city: Dublin

first: Brendan

last: Loftus

address: Conway Institute, Belfield, Dublin 4

department: School of Medicine & Medical Science

country: Ireland

institute: University College Dublin

summary: The objective of this study is to develop an integrated map for the M. abscessus ATCC19977 organism. Among the data types contributing to the development of this map are next-generation RNA-sequencing, differential RNA-sequencing, ribosome profiling, and mass spectrometry.

overall_design: The design of the study consists of two biological samples, each with one technical replication; both biological samples were subjected to identical conditions.

first: Aleksandra

middle: M

last: Luengo

first: Adam

last: Dinan

first: Anna

last: Aulicino

first: Patrick

last: Staunton

first: Laura

last: Ardill

first: Tong

last: Pin

first: Amanda

last: Lohan

first: Steve

last: Gordon

first: Kevin

last: Conlon


title: ChIP-Seq of Klf6 in oligodendrocytes

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We examine the role of Klf6 in oligodendrocyte progenitor cells and determine that Klf6 acts in part through direct regulation of gp130 signaling and nuclear import via  importin-α5 (Impα5), a key controller of nuclear trafficking.

overall_design: Examination of Klf6 DNA binding in two different stages of differentiation


title: Differentially expressed genes after miRNA or siRNA transfection in human cancer cell lines (II)

status: Public on Apr 13 2016

city: Chiba

first: Naohiko

last: Seki

state: Chiba

address: 1-8-1, Inohana

department: Functional Genomics

institute: Chiba University

summary: To identify differentially expressed genes by anti cancer treatments (microRNAs or siRNAs) in human cancer, several cell lines (bladder cancer, prostate cancer, renal cell carcinoma, oral squamous cell carcinoma and lung squamous cell carcinoma) were subjected to Agilent whole genome microarrays.

overall_design: Human cancer cell lines (SAS, HSC3, BOY, T24, PC3, PC3M, DU145, C4-2, 786-O, A-498 and EBC-1) were treated with miRNAs (miR-205, miR-29a, miR-144-3p, miR-144-5p, miR-451, miR-210, miR-145-5p, miR-145-3p, miR-23b cluster, miR-221, miR-222 and miR-223), siRNAs (si-GOLM1, si-HMGB3, si-CENPF, si-LOXL2, si-TMEM184B and si-CORO1C).


title: Chronic Intermittent Ethanol by vapor chamber gene expression time-course in hippocampus [HPC]

first: Howard

first: Maren

last: Smith


title: Genome-wide profiling of SWI/SNF chromatin remodeler BRAHMA and Histone H3 lysine demethyalse Relative of Early Flowering 6 (REF6) in Arabidopsis [RNA-Seq]

status: Public on Mar 28 2016

city: shenzhen

first: Lei

last: Gao

state: guangdong

address: Nanhai Ave 3688

department: College of Life Sciences

country: China

institute: shenzhen university

summary: BRAHMA (BRM) is a conserved SWI/SNF-type chromatin remodeling ATPase implicated in many key nuclear events. Histone H3 Lysine 27 (H3K27) demethylases specifically remove the repressive histone mark, trimethylation of H3K27 (H3K27me3). Both proteins are thought to play active roles in regulating gene activities at the chromatin level, but their genome-wide coordination remains to be determined. In Arabidopsis thaliana, RELATIVE OF EARLY FLOWERING 6 (REF6, also known as JMJ12) is the first identified plant H3K27 demethylase. Here, genome-wide analyses revealed that REF6 targets to thousands of genes across the Arabidopsis genome and co-localizes with BRM at more than 1,000 genes, many of which are genes involved in response to various stimuli, especially plant hormones. Loss of REF6 activity results in decreased BRM occupancy at hundreds of BRM-REF6 co-targets, indicating that REF6 is required for the recruitment of BRM to chromatin. Further, REF6 targets to genomic loci that contains the CTCTGTTT motif in vivo through its C2H2 zinger finger domains. Consistently, the two proteins activate the expression of a set of common genes in plant cells. Thus, this work demonstrates a genome-wide coordination between an H3K27me3 demethylase and a chromatin remodelling protein.

overall_design: Examination of global RNA expression in 14-day-old wt, brm-1, ref6-1 and brm-1 ref6-1 seedlings. Three biological replicates for each one.

first: Chenlong

last: Li

first: Yuhai

last: Cui


title: Chronic Intermittent Ethanol by vapor chamber gene expression time-course in five brain regions

first: Michael

last: Miles


title: Effect of Anaplasma phagocytophilum infection on the micro RNA profile of Ixodes scapularis tick cells

status: Public on Mar 19 2016

city: Ciudad Real

first: Jose

last: De La Fuente

state: Ciudad Real

address: Ronda de Toledo s/n

country: Spain

institute: SaBio. Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM

summary:
Ticks are blood feeding arthropod ectoparasites that transmit pathogens, which cause diseases in humans and animals worldwide. In the past ten decades, the continuous human exploitation of environmental resources and the increase in human outdoor activities has promoted contact with arthropod vectors normally present in the wild, resulting in increased transmission of vector-borne pathogens. In addition, vector populations are expanding in response to climate change and human interventions that impact reservoir host movement and human exposure to infected vectors. Among these emerging vector-borne pathogens, Anaplasma phagocytophilum (Rickettsiales: Anaplasmataceae) has become an important tick-borne pathogen in the United States, Europe and Asia, with increasing numbers of infected people and animals every year. Diseases caused by A. phagocytophilum include human granulocytic anaplasmosis (HGA), equine and canine granulocytic anaplasmosis and tick-borne fever (TBF) in ruminants.
The natural infection cycle of A. phagocytophilum is dependent upon the presence of infected vertebrate reservoir hosts and Ixodid tick vectors. In the United States and Europe the main vector species are Ixodes scapularis, Ixodes pacificus, and Ixodes ricinus, while a wide range of mammals, lizards, and birds serve as reservoir hosts for various A. phagocytophilum genotypes. A. phagocytophilum initially infects tick midgut cells  and then subsequently develops in salivary glands for transmission to susceptible hosts during tick feeding where the pathogen infects granulocytic cells, primarily neutrophils.
Anaplasma phagocytophilum develops within membrane-bound inclusions in the host cell cytoplasm. This pathogen has evolved with its tick and vertebrate hosts through dynamic processes involving genetic traits of the pathogen and hosts that collectively mediate pathogen infection, development, persistence, and survival. However, the mechanisms used by A. phagocytophilum for molecular mechanisms involved in tick-pathogen interactions have not been fully characterized.
The objective of this study is to characterize the dynamics of the microRNA response in the tick vector Ixodes scapularis in response to A. phagocytophilum infection. To address this objective, the composition of tick microRNAs was characterize using RNA sequencing in I. scapularis tick cells in response to A. phagocytophilum infection.
The discovery of these mechanisms provides evidence that a control strategy could be developed targeted at both vertebrate and tick hosts for more complete control of A. phagocytophilum and its associated diseases.

overall_design: Samples infected with Anaplasma phagocytophilum NY18 (ISE6-NY5) and uninfected controls.

first: Pilar

last: Alberdi

first: Pedro

last: Espinosa

first: Margarita

last: Villar

first: Marina

last: Manrique

first: Raquel

last: Tobes

first: José

last: de la Fuente


title: Examining the role of Klf6 in oligodendrocyte progenitor cells using ChIP-Seq and RNA-Seq

first: Gareth

last: John


title: Effect of LPS and glutathione depletion on gene expression profiling in mouse macrophage-like cells

city: Brighton

first: Pietro

last: Ghezzi

address: BSMS Teaching Building

institute: Brighton & Sussex Medical School

summary: By microarray gene expression profiling, we investigated whether glutathione (GSH) has a signaling role in the response of RAW 264.7 cells to lipopolysaccharide (LPS). GSH was depleted by prior incubation with 120 µM buthionine sulfoximine (BSO) for 24 h, then cells were treated with 10 ng/ml LPS for 2 or 6 h. DNA microarray analysis was performed in triplicate samples in control and GSH-depleted cells, in the presence or absence of LPS.

overall_design: 4 conditions, 3 replicates, at 2 h and 6 h

last: Diotallevi

first: Manuela

last: Mengozzi


title: Hormonal and epigenetic control of hematopoiesis

city: Chicago

first: Aparna

last: Vasanthakumar

state: IL

address: 900 E.57th Street, KCBD

department: Medicine

institute: The University of Chicago

summary: To study the role of epigenetics and hormones on hematopoietic stem cell function, hematopoietic stem and progenitor (LSK) cells were sorted from E14.5 embryos of wild-type, DNMT3B7 hemizygous or DNMT3B7 homozygous genotype. The expression analysis was performed to provide information regarding the mechanism by which hormones regulate hematopoiesis.

overall_design: Hematopoietic stem and progenitor (LSK) cells from E14.5 murine embryonic fetal livers of wild-type, or DNMT3B7 transgenic genotypes were flow-sorted, and RNA isolated for expression analysis by RNA-Sequencing

first: Vasanthakumar

last: Aparna

first: Lucy

last: Godley


title: Identification of a serum six-microRNA panel as potential noninvasive biomarker for meningioma

status: Public on Apr 12 2016

city: Changzhou

first: Yilin

last: Yang

state: Jiangsu

address: 185#, Juqian Road

department: Modern Medical Research Center

institute: Third Affiliated Hospital of Soochow University

summary:
TaqMan low density array (TLDA) was carried out to screen of the profiles of circulating miRNAs in pooled serum samples from healthy controls and pre-operative meningioma patients.
The expression changes of circulating miRNAs in meningioma patients were identified.

overall_design: To select candidate serum miRNAs for meningioma detection and monitoring, we employed TLDA technique to screen expression levels of 739 miRNAs in pooled serum samples from healthy controls and pre-operative meningioma patients (each pooled from 20 individuals).

first: Feng

last: Zhi


title: microRNA expression profile between KRAS/BRAF wild and BRAF mutant colorectal cancer

city: sendai

first: Hidekazu

last: Takahashi

address: Seiryo-machi 4-1, Aoba-ku

department: Department of clinical oncology

institute: Institute of Development, Aging and Cancer, Tohoku University

summary: The genome-wide miRNA expression analysis was performed in clinical samples, comprising 15 BRAF-mutant and 15 non-KRAS/BRAF-mutant colorectal cancers by using a SurePrint G3 Human miRNA microarray.

first: Masanobu


title: Genome-wide profiling of SWI/SNF chromatin remodeler BRAHMA and Histone H3 lysine demethyalse Relative of Early Flowering 6 (REF6) in Arabidopsis

status: Public on Mar 29 2016

first: Lei

last: Gao


title: Genome-wide profiling of SWI/SNF chromatin remodeler BRAHMA and Histone H3 lysine demethyalse Relative of Early Flowering 6 (REF6) in Arabidopsis [ChIP-Seq]

summary: BRAHMA (BRM) is a conserved SWI/SNF-type chromatin remodeling ATPase implicated in many key nuclear events. Histone H3 Lysine 27 (H3K27) demethylases specifically remove the repressive histone mark, trimethylation of H3K27 (H3K27me3). Both proteins are thought to play active roles in regulating gene activities at the chromatin level, but their genome-wide coordination remains to be determined. In Arabidopsis thaliana, RELATIVE OF EARLY FLOWERING 6 (REF6, also known as JMJ12) is the first identified plant H3K27 demethylase. Here, genome-wide analyses revealed that REF6 targets to thousands of genes across the Arabidopsis genome and co-localizes with BRM at more than 1,000 genes, many of which are genes involved in response to various stimuli, especially plant hormones. Loss of REF6 activity results in decreased BRM occupancy at hundreds of BRM-REF6 co-targets, indicating that REF6 is required for the recruitment of BRM to chromatin. Further, REF6 targets to genomic loci that contains the CTCTGTTT motif in vivo

sample_organism:
Arabidopsis
Arabidopsis thaliana

platform_organism:
Arabidopsis
Arabidopsis thaliana

overall_design: Examination of BRM occupancy in 14-day-old wt and ref6-1 seedlings. Examination of REF6 occupancy in 14-day-old wt and brm-1 seedlings. Examination of global RNA expression in 14-day-old wt, brm-1, ref6-1 and brm-1 ref6-1 seedlings. Examination of H3K27me3 profiles in 14-day-old wt, brm-1, ref6-1, and brm-1 ref6-1 seedlings.

first: Chenlong

last: Li

first: Yuhai

last: Cui


title: Vldlr KO vs Jax WT Array

status: Public on Mar 14 2016

city: Boston

first: Lois

last: Smith

state: MA

address: 300 Longwood Avenue

department: Ophthalmology

institute: Harvard Medical School

summary: Analysis of lipid metabolism at gene expression level.

overall_design: Total RNA obtained from isolated retinas from Vldlr ko mice and Jax WT mice

first: Jean-Sebastien

last: Joyal


title: Therapy-Induced Developmental Reprogramming of Prostate Cancer Cells and Acquired Resistance [Dataset 2]

status: Public on Mar 11 2016

city: Vancouver

first: Shawn

last: Anderson

state: BC

address: 2660 Oak Street

country: Canada

institute: Vancouver Prostate Centre

summary: Treatment-induced neuroendocrine transdifferentiation (NEtD) complicates therapies for metastatic prostate cancer (PCa). Based on evidence that PCa cells can transdifferentiate to other neuroectodermally-derived cell lineages in vitro, we proposed that NEtD requires first an intermediary reprogramming to metastable cancer stem-like cells (CSCs) of a neural class and we demonstrate that several different AR+/PSA+ PCa cell lines were efficiently reprogrammed to, maintained and propagated as CSCs by growth in androgen-free neural/neural crest (N/NC) stem medium. Such reprogrammed cells lost features of prostate differentiation; gained features of N/NC stem cells and tumor-initiating potential; were resistant to androgen signaling inhibition; and acquired an invasive phenotype in vitro and in vivo. When placed back into serum-containing mediums, reprogrammed cells could be re-differentiated to N-/NC-derived cell lineages or return back to an AR+ prostate-like state. Once returned, the AR+ cells were resistant to androgen signaling inhibition. Acute androgen deprivation or anti-androgen treatment in serum-containing medium led to the transient appearance of a sub-population of cells with similar characteristics. Finally, a 132 gene signature derived from reprogrammed PCa cell lines distinguished tumors from PCa patients with adverse outcomes. This model may explain neural manifestations of PCa associated with lethal disease.  The metastable nature of the reprogrammed stem-like PCa cells suggests that cycles of PCa cell reprogramming followed by re-differentiation may support disease progression and therapeutic resistance. The ability of a gene signature from reprogrammed PCa cells to identify tumors from patients with metastasis or PCa-specific mortality implies that developmental reprogramming is linked to aggressive tumor behaviors.

overall_design: Gene expression profiles were obtained for RNAs extracted from biological replicates of parental LNCaP cells or from Neuroendocrine-like LNCaP (LNCaP-NE) cells grown for 15 days in CSS-media with no androgen.

first: Mengqian

last: Chen

first: Josselin

last: Caradec

first: Amy

last: Lubik

first: Ralph

last: Buttyahn


title: IL-31 regulation of transcripts in skin

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

summary: Interleukin-31 (IL-31), a T cells derived cytokine which is mainly produced by CD4+ T cells skewed towards Th2 phenotypes. It signals via a heterodimeric receptors composed of IL-31RA and OSMR that is expressed constitutively in epithelial cells and keratinocytes. IL-31 is shown to play a pathogenic role in allergic and inflammatory diseases. Transgenic mice overexpressing IL-31 have a phenotype similar to atopic dermatitis.  Here, we studied the role of IL-31 in skin damage by intradermal administration of recombinant IL-31. Notably, IL-31 was sufficient to increase epidermal basal cell proliferation and thickening of the epidermal layer of skin in mice. Analysis of skin transcriptome indicates a significant increase in the transcripts involved in epidermal cell proliferation and pathological skin remodeling. Thus, our study revealed an important role of IL-31 signaling in activating transcriptional programs involved in the pathophysiology of skin diseases.

overall_design: mRNA profiles of C57BL/6 mice skin injected with saline and rIL-31 (20µg) via i.d.

first: Satish

last: Madala


title: Gene expression profiles during human lung tumorigenesis

city: Beijing

first: Run

last: Tong

address: 17# Pan Jia Yuan Nan Li, Chao Yang District, P.O. Box 2258

department: Department of Etiology and Carcinogenesis

institute: Cancer Hospital and Institute, Chinese Academy of Medical Sciences and Peking Union Medical College

summary: Some tumor initiation processes as well as genetic and genomic changes during human lung tumorigenesis have been progressively revealed. In our study, we elucidated expression profiles in normal human airway epithelium cells from non-smokers, immortalized human bronchial epithelial cell lines and lung squamous cell carcinoma tissues. Collectively, these cells reflect a progressively increasing degree of malignancy. Furthermore, from its earliest stages, lung tumorigenesis may be associated with decreased IFN alpha/beta signaling, and this association may provide insights for the selection of high-risk lung cancer patients.

overall_design:
The study material for human lung tumorigenesis consisted of 73 cases of normal human airway epithelium cells from non-smokers, 8 cases of immortalized human bronchial epithelial cell lines and 69 cases of lung squamous cell carcinoma tissues. All the airway epithelium cells were examined with Agilent SurePrint G3 Human GE v2 8x60K Microarray (G4851B), and the immortalized human bronchial epithelial cell lines and lung squamous cell carcinoma tissues were examined with Agilent Whole Human Genome Microarray 4x44K (G4112F).

Please note that data were independently processed in two groups;
GPL17077-hybridized samples GSM1637811-GSM1637883
GPL6480-hybridized GSM1637884-GSM1637960

first: Lin

last: Feng

last: Zhang

first: Jianzhi

first: Yousheng

last: Mao

first: Kaitai

first: Yanning

first: Guiqi

last: Wang

first: Shujun

last: Cheng


title: Direct Induction of Neurons from Various Cell Types by Chemical Defined Medium

status: Public on Mar 17 2016

city: Guangzhou

first: Hao

last: Sun

address: Kaiyuan avenue 190

institute: GIBH

summary: We have developed a serum-free chemical defined medium, namely 6C, that can directly convert mouse embryonic fibroblast (MEFs), glia cells into neurons in vitro. Human cells such as human foreskin fibroblast(HHFs), Hela cells and born marrow derived mesenchymal stem cells (BM-hMSC) can also be converted into neuron-like cells by this medium with some modification such as including several other small molecules. To understand the possible mechanisms, the transdifferentiation of MEFs by 6C was chosen as a model system and gene profiling at different time point during the conversion was carried out by RNA sequencing using Illumina MiSeq. MEFs was maintained in MEF medium (DMEM containing 10% FBS, 1mM Glutamax and 100X NEAA), to start the induction, the culture medium was shift to 6C and marked as day 0, neurons could be generated in day 15. mRNA samples was collected at day 0, 2, 5, 10, 15 during the process, with cell lysed by Trizol and mRNA enriched by Illumina TruSeq RNA Sample Preparation v2 kit. We find that most cell cycle related genes were up regulated during the first few days of induction, while many Notch pathway genes up regulated during the later phase of this process. The RNA sequencing data provided important cues for further study on the mechanisms of the direct neuronal induction process.

overall_design: Gene profiling at different time point during the transdifferentiation mediated by 6C medium.

first: Hui

last: Zheng


title: Pathway implications of aberrant global methylation in adrenocortical cancer

status: Public on Mar 07 2016

city: Phoenix

first: Bodour

last: Salhia

state: AZ

address: 445 N Fifth Street

department: Integrated Cancer Genomics Division

institute: Translational Genomics Research Institute

summary:
Context: Adrenocortical carcinomas (ACC) are a rare tumor type with a poor five-year survival rate and limited treatment options.   Objective: Understanding of the molecular pathogenesis of this disease has been aided by genomic analyses highlighting alterations in TP53, WNT, and IGF signaling pathways. Further elucidation is needed to reveal therapeutically actionable targets in ACC.
Design: In this study, global DNA methylation levels were assessed by the Infinium HumanMethylation450 BeadChip Array on 18 ACC tumors and 6 normal adrenal tissues.  A new, non-linear correlation approach, the discretization method, assessed the relationship between DNA methylation/gene expression across ACC tumors.
Results: This correlation analysis revealed epigenetic regulation of genes known to modulate TP53, WNT, and IGF signaling, as well as tumor suppressor silencing previously unreported in ACC.
Conclusions: DNA methylation may regulate genes known to play a role in ACC pathogenesis as well as known tumor suppressors.

overall_design: Bisulphite converted DNA from 24 samples were hybridized to the HumanMethylation450 BeadChip.

first: Christophe

last: Legendre

first: Chris

last: Gooden


title: lncRNA expression profile identified by microarray in infantile hemangioma

status: Public on Mar 03 2016

city: Jinan

first: Xiaowen

last: Liu

state: Shandong

address: Jingwu Road 324

institute: Shandong Provincial Hospital affiliated to Shandong University

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

summary: Infantile hemangioma (IH) was one of the most common vascular tumors during childhood. Long non coding RNAs (lncRNAs) play great roles in angiogenesis; the involvement of lncRNAs in hemangioma remains unknown. We aim to investigate the differential expression of lncRNA between hemangioma and the adjacent normal tissues, with a view to studying the biological function of lncRNAs and their involvement in the pathogenesis of hemangioma. The differential lncRNAs expression profiles of hemangioma were established by lncRNA microarray. Bioinformatic analyses were applied for further study of these differentially expressed lncRNAs. A total of 2116 differentially expressed lncRNAs were identified, among these lncRNAs, 1259 were up-regulated and 857 were down-regulated more than two-fold.

overall_design: Two-conditioned experiment, hemangioma tissue VS adjacent non-tumor skin tissue. Biological replicates: 3 infantile hemangioma tissue, 3 adjacent non-tumor skin tissue. Three samples of infantile hemangioma were included in the study, and the adjacent nontumor skin tissues were identified as control. One replicate per sample.

first: Ran

last: Huo


title: Next generation sequencing profiling identifies miR-574-3p and miR-660-5p as potential novel prognostic markers for breast cancer

status: Public on Mar 02 2016

city: Edmonton

first: Sambasivarao

last: Damaraju

state: Alberta

address: 11560 University Ave

department: Laboratory medicine and pathology

institute: University of Alberta

summary: Prognostication of Breast Cancer (BC) relies largely on traditional markers such as hormone or growth factors but due to their suboptimal specificities, it is challenging to identify the subset of patients who are likely to undergo recurrence and markers of higher specificity are sought to guide therapies. MicroRNAs (miRNAs) are small non-coding RNAs which function as post-transcriptional regulators of gene expression and have shown promise as potential prognostic markers in several cancer types including BC. In our study, we sequenced 104 breast tumor tissue samples and 11 apparently healthy normal breast tissues for miRNAs. Two widely used approaches were adopted to identify prognostic markers – Case-control and Case-only. For both the approaches, Cox-proportional hazards regression model and risk score analysis was performed to identify miRNA signature independent of potential confounders. Representative miRNAs were validated using qRT-PCR. Gene ontology terms were identified for miRNAs significant in survival analysis. A total of 1,423 miRNAs were captured from the tissues, of which 126 were retained with predetermined criteria for good read counts. In the case-control approach, 80 miRNAs were differentially expressed, from which four and two miRNAs were significant for OS and RFS respectively. In the case-only approach, from 147 miRNAs, 11 and four miRNAs were significant for OS and RFS respectively, in which miR-574-3p and miR-660-5p were novel and were not previously found to be associated with BC prognosis.  Multivariate Cox analysis indicated that the risk scores calculated in both the approaches were potential independent prognostic factors for BC. Targets for the identified miRNAs were enriched for cell proliferation, invasion and migration.

overall_design: Identification of miRNAs as prognostic markers for breast cancer

first: Preethi

last: Krishnan

first: Sunita

last: Ghosh

first: Bo

first: Dongping

last: Li

first: Ashok

last: Narasimhan

first: Richard

last: Berendt

first: Kathryn

last: Graham

first: John

last: Mackey

first: Olga

last: Kovalchuk


title: RNAseq Reveals Virulence-Specific Host Responses to M. tuberculosis infection

status: Public on Mar 01 2016

city: Bellville

first: Abhilasha

last: Madhvi

state: Western Cape

address: Francie van Zijl Drive. Tygerberg

country: South Africa

institute: Stellenbosch University

summary: We infect bone marrow derived macrophages (BMDMs) with either a Hyper or Hypovirulent Mycobacterium tuberculolsis strain and assess the host response to these bacteria through RNAseq

overall_design: Uninfected BMDMs served as controls, BMDMs infected with Hypervirulent M.tb (designated R55), BMDMs infected with Hypovirulent m.tb (designated R50). 3 groups with 3 biological replicates, each analysed in triplicate.

first: G

last: Leisching

first: B

last: Baker


title: Therapy-Induced Developmental Reprogramming of Prostate Cancer Cells and Acquired Resistance

first: Shawn

last: Anderson

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

overall_design: Refer to individual Series


title: High-throughput sequencing and degradome analysis reveal two distinct evolutionary patterns of Cercis gigantea microRNAs and their targets

status: Public on Mar 10 2016

city: ShangHai

first: Liucun

last: Zhu

state: ShangHai

address: Room 402, No. 17, ShangDa Road

institute: Shanghai University

summary: In this study, C. gigantea miRNAs and their target genes were investigated by extracting RNA from young roots, tender stems, young leaves, and flower buds of C. gigantea to establish a small RNA (sRNA) library and a degradome library to further sequence. This study identified 194 known miRNAs belonging to 52 miRNA families and 23 novel miRNAs. Among the miRNA families, 158 miRNAs from 27 miRNA families were highly conserved and existed in a plurality of plants. In addition, 60 different targets for 30 known families and one target for novel miRNA were identified by high-throughput sequencing and degradome analysis in C. gigantea. Our analyses showed that conserved miRNAs have higher expression levels and more family members as well as more targets than other miRNAs. Meanwhile, these conserved miRNAs were found to be involved in auxin signal transduction, regulation of transcription, and other developmental processes in plants, which will help further understanding regulatory mechanisms of C. gigantea miRNAs.

overall_design: The samples were collected from the young roots, tender shoots, young leaves and flower buds of wild C. gigantea growing in Jiangsu Province. TRIzol reagent (Invitrogen, USA) was used to extract the total RNAs [20]. An Illumina next-generation sequencing system, i.e. the 1 G Genome Analyzer sequencing platform, was utilized for sRNA sequencing. An Illumina HiSeq 2000 (LC Sciences, USA) was used for degradome sequencing.

first: Wenna

last: Guo


title: POU2AF1 Functions in the Human Airway Epithelium to Regulate Expression of Host Defense Genes

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College


title: Genome-wide gene expression and DNA methylation reveals Genetic and Epigenetic differences in cloned piglets and conventionally  bred normal piglets (RNA-Seq)

status: Public on Feb 26 2016

city: Wuhan

first: Changchun

state: Hu Bei

address: No.1, Shizishan Street · Hongshan District

institute: Huazhong Agriculture University

summary:
Somatic cell nuclear transfer has brought considerable chances to breed excellent breeds and protect endanger animals, while also produced numerous fail embryos and abnormal individuals due to inefficient epigenetic modification at the same time. To understand some mechanisms of abnormal piglets with phenotypes such as macroglossia, standing and walking disabilities in our study and find some differences between abnormal piglets and conventionally bred normal piglets, DNA methylation profile and genome-wide gene expression were conducted in two groups, using methylated DNA immunoprecipitation binding highthroughput sequencing (MeDIP-Seq) and RNA sequencing(RNA-Seq).
We generated and provided a genome-wide DNA methylation and gene expression profile for abnormal cloned and conventionally bred piglets.  We detected a total of 1493 genes differentially expressed in two groups and 382 of these genes also differentially methylated in two groups. Analysis of relationship between DNA methylation and gene expression revealed that DNA methylation levels had significantly negative and monotonic correlation with gene expression levels in particular regions of genes while no obvious monotonic correlation in other regions. Besides, we found some interesting genes and pathways such as MYH7 and mTOR signalling pathway that may played essential role in muscle growth and development. Briefly, these results provide reliable data for future epigenetic studies and may help to uncover the mechanism of failure clones via SCNT.

overall_design:
We dissected the leg muscle from the cloned piglets and the conventionally bred piglets, and analyzed the difference of MeDIP-seq and RNA-seq between the two groups.
As for data of abnormal cloned piglets, we downloaded it from GEO under Super-Series accession No. GSE51477, including SubSeries accession No.GSE51282 for RNA-seq data (No. GSM1241829 for abnormal cloned group) and SubSeries accession No. GSE51476 for MeDIP-seq data (No. GSM1246252 for abnormal cloned group).

first: Cheng

last: Zou

first: Chuangchun


title: Genome-wide gene expression and DNA methylation reveals Genetic and Epigenetic differences in cloned piglets and conventionally bred normal piglets

type: Methylation profiling by high throughput sequencing


title: POU2AF1 Functions in the Human Airway Epithelium to Regulate Expression of Host Defense Genes [array]

summary:
In the process of seeking novel lung host defense regulators by analyzing genome-wide RNA sequence data from normal human airway epithelium, we detected expression of POU2AF1, a known transcription co-factor previously thought to be expressed only in lymphocytes. Lymphocyte contamination of human airway epithelial samples obtained by bronchoscopy and brushing was excluded by immunohistochemistry staining, the observation of up-regulation of POU2AF1 in purified airway basal stem/progenitor cells undergoing differentiation and analysis of differentiating single basal cell clones. Lentivirus-mediated up-regulation of POU2AF1 in airway basal cells induced up-regulation of host defense genes, including MX1, IFIT3, IFITM and known POU2AF1 downstream genes HLA-DRA, ID2, ID3, IL6, BCL6. Interestingly, expression of these genes paralleled changes of POU2AF1 expression during airway epithelium differentiation in vitro, suggesting POU2AF1 helps to maintain a "host defense tone" even in pathogen-free condition. Cigarette smoke, a known risk factor for airway infection, suppressed POU2AF1 expression both in vivo in humans and in vitro in human airway epithelial cultures, accompanied by deregulation of POU2AF1 downstream genes. Finally, enhancing POU2AF1 expression in human airway epithelium attenuated the suppression of host defense genes by smoking. Together, these findings suggest a novel function of POU2AF1 as a potential regulator of host defense genes in the human airway epithelium.
Methods: Massive parallel RNA sequencing was used to compare the transcriptome of lentivirus mediated POU2AF1 or RFP (control) gene expression in human primary airway epithelial cells (3 samples per group). Uninfected basal cell was used as a further control.
Conclusions: The genes up-regulated by POU2AF1 in human airway epithelial cells are mainly related to the intracellular or extracellular anti-pathogen response, suggesting POU2AF1 plays a role in airway epithelial host defense.

overall_design: This Series represents samples complementary to those in GSE60989.


title: Therapy-Induced Developmental Reprogramming of Prostate Cancer Cells and Acquired Resistance [Dataset 1]

overall_design: To compare gene expression between parental PCa cells and STM-reprogrammed cells (LNCaP, VCaP, CWR-22rv1 and LAPC4), RNAs from biological triplicate samples of parental cells and corresponding STM-reprogrammed cells (>14 days in STM) were extracted.

first: Josselin

last: Caradec

first: Amy

last: Lubik

first: Mannan

last: Nouri

first: Ralph

last: Buttyan


title: Genome-wide gene expression and DNA methylation reveals Genetic and Epigenetic differences in cloned piglets and conventionally  bred normal piglets (MeDIP-Seq)

last: Li


title: Quantitative Analysis of Notch mutant (Notch1&2-null, Psen1&2-null, RBPjk-null) and wild-type hair follicle transcriptomes by NGS

status: Public on Feb 29 2016

first: Raphael

last: Kopan

state: Ohio

address: 3333 Burnet Avenue

department: Developmental Biology

institute: Cincinnati Children's Hospital

summary: The goals of this study is to test whether NICD presence protects the RBPjk-null Hair Follicles by altering gene expression via association with other DNA binding proteins at P3, just before the conversion to TSLP-producing keratin cysts.

overall_design:
Methods: Skin samples were embedded in OCT. Sectioned at 20μm thickness. Dehydrated in EtOH, and equilibrated to Xylene before the LCM procedure. Laser capture was performed with Arcturus Veritas.
Methods: ~100 hair follicles from Notch-null, PS-null, RBPjk-null and wild-type samples were pooled into 3 biological replicates for each genotype and subjected to RNA isolation followed by RNA-Seq.
Conclusions: A total of 2047 genes were differentially expressed (≥1.5 fold) in three or more biological replicates of Notch mutant hair follicles compared to wild-type controls (p-value<0.05). Unsupervised hierarchical clustering analysis failed to distinguish between the mutants.

first: Turkoz

last: Mustafa

first: Kopan

last: Raphael


title: Hepatic gene expression data from A/J mouse and A/J-12SM consomic mouse

city: Nagoya

first: Misato

last: Kobayashi

state: Aichi

address: Furo-cho, Chikusa-ku

department: Graduate School of Bioagricultural Sciences

institute: Nagoya University

summary:
SMXA-5 mouse shows a high-fat induced fatty liver. The QTL for fatty liver was mapped on mouse chromosome 12, designated as Fl1sa. The liver triglycerides content of A/J-12SM consomic mouse, a chromosome substitution strain, was suppressed  compared to that of A/J mouse.
We compared the hepatic gene expressions between A/J mouse and A/J-12SM consomic mouse.

overall_design: Total RNA of male A/J mice and A/J-12SM consomic mice fed a high-fat diet for 7weeks were extracted individually from liver of nine mice.   The RNAs from three mice were pooled and hybridized on one Affimetrix microarray. Sample were analyzed in triplicate set of array (three biological replicates).

first: Chie

last: Taguchi

first: Atsushi

last: Murai

first: Fumihiko

last: Horio


title: Identification of copper (Cu) stress-responsive grapevine microRNAs and their target genes by high-throughput sequencing

status: Public on Feb 20 2016

city: Nanjing

first: Songtao

last: Jiu

address: Weigang 1

department: College of Horticulture

institute: Nanjing Agricultural University

summary:
Background: MicroRNAs (miRNAs) are a class of single-stranded non-coding small RNAs (sRNAs) that are 20-24 nucleotides (nt) in length. Extensive studies have indicated that miRNAs play important roles in plant growth, development, and stress responses. With more copper (Cu) and copper-containing compounds used as bactericides and fungicides in viticulture, Cu stress has become one of the serious environmental problems that affect plant growth and development. In order to uncover the hidden response mechanisms of Cu stress, many Cu-responsive miRNAs have been detected in several plant species. However, there have been few reports about the grapevine miRNAs in response to Cu.

Results: Here, two small RNA libraries were constructed from Cu-treated and water-treated (control) leaves of 'Summer Black' grapevine. Following high-throughput sequencing and filtering, 158 known vvi-miRNAs and 98 novel vvi-miRNAs were identified in the two libraries. Among these, 24 could only be detected in the treatment, and 63 were only detected in the control. Additionally, 100 known vvi-miRNAs were found to be clearly responsive to Cu, among which 96 were down-regulated and four were up-regulated; 47 novel vvi-miRNAs were found to be clearly responsive to Cu, among which 35 were down-regulated and 12 were up-regulated. Subsequently, expression patterns of a set of Cu-responsive vvi-miRNAs were validated by quantitative real-time PCR (qRT-PCR). There existed some consistency in expression levels of Cu-responsive vvi-miRNAs between high-throughput sequencing and qRT-PCR assays. In addition, 92 putative targets for 79 known vvi-miRNAs and 51 putative targets for 22 novel vvi-miRNAs were predicted, and most of the targets are involved in multiple biological processes including transcriptional regulation and response to biotic and abiotic stresses.

Conclusions: In this study, 147 Cu-responsive vvi-miRNAs were identified using high-throughput sequencing, and their target genes were predicted, which will be helpful to understanding the molecular mechanisms of miRNAs in response to Cu stress. Furthermore, this work can also provide a foundation for further study of the networks of miRNAs involved in grapevine plant growth and breeding some Cu-tolerant grapevine cultivars.

overall_design: Mixed 'Summer Black' grapevine young leaves (2 weeks old), large leaves (5 weeks old), and old leaves (9 week old) in randomly-selected plants from both the Cu-treated and control groups were collected for high-throughput sequencing. Subsequently, we carried out the analysis of Solexa sequencing data, and performed the research of regulatory modes of grapevine miRNAs on their target genes during Cu stress.

first: Xiangpeng

last: Leng

first: Zhenqiang

last: Xie

first: Xiaopeng

first: Xiaomin

last: Wang

first: Tariq

last: Pervaiz

first: Jun

last: Lu

first: Lingfei

last: Shangguan

first: Jinggui

last: Fang


title: Comprehensive Epigenomic Analysis Reveals Dynamic Regulatory Programs Of Blood Development (Dnase-Hypersensitivity)

city: Leeds

first: MS

last: Vijayabaskar

address: Woodhouse Lane

department: School of Molecular and Cellular Biology

institute: University of Leeds

summary: Embryonic hematopoiesis is regulated by the coordinated interaction between transcription factors and the epigenetic regulators driving developmental-stage specific gene expression but how this process drives hematopoietic specification and terminal differentiation is poorly understood. Here we generated RNA-Seq, DNase-Seq and ChIP-Seq data for histone marks and transcription factors from ES-cell derived purified cells representing six sequential stages of blood cell specification and differentiation. Our data reveal the binding patterns of specific transcription factors involved in the priming and maintenance of distal elements and inform how binding impacts on promoter activity. Functional studies based on these data uncovered a previously unrecognised role for Hippo signalling in mammalian hematopoietic specification. Finally, we present a dynamic core regulatory network model for hematopoiesis and demonstrate its utility for the design of reprogramming experiments. Our study represents a powerful resource for studying hematopoiesis and demonstrates how such data can advance our understanding of mammalian development.

overall_design: ChIP-seq data of histone modifications and transcription factors, and RNA-seq data obtained from purified cells representing five sequential stages of murine blood cell specification and differentiation

first: Debbie

last: Goode

first: Nadine

last: Obier

first: M

first: Monika

last: Lichtinger

first: Michael

last: Lie-A-Ling

first: Rebecca

last: Hannah

first: Andrew

middle: J

last: Lilly

first: Magdalena

last: Florowska

first: Kiran

last: Batta

first: Mairi

last: Challinor

first: Kirstie

last: Wallace

first: Salam

last: Assi

first: Pierre

last: Cauchy

first: Jane

last: Gilmour

first: Maarten

last: Hoogenkamp

first: David

last: Westhead

first: Georges

last: Lacaud

first: Valerie

last: Kouskoff

first: Berthold

last: Göttgens

first: Constanze

last: Bonifer


title: Comprehensive Epigenomic Analysis Reveals Dynamic Regulatory Programs Of Blood Development (TF ChIP-seq)

first: MS

last: Vijayabaskar

first: Debbie

last: Goode

first: Nadine

last: Obier

first: Monika

last: Lichtinger


title: Comprehensive Epigenomic Analysis Reveals Dynamic Regulatory Programs Of Blood Development (ChIP-seq)

first: M

first: Michael

last: Lie-A-Ling

first: Rebecca

last: Hannah

first: Andrew

last: Lilly

first: Magdalena

last: Florowska


title: RNA-sequencing reveals transcriptional up-regulation of Trem2 in response to bexarotene treatment

status: Public on Feb 19 2016

city: Pittsburgh

first: Iliya

last: Lefterov

state: PA

address: 100 technology drive

department: Department of environmental and occupational health

institute: University of Pittsburgh

summary: High throughput massively parallel sequencing on mRNA libraries generated from cortices of bexarotene or vehicle treated APP/PS1

overall_design: Read counts analyzed for differential gene expression using edgeR

first: Jonathan

last: Schug

first: Radosveta

last: Koldamova


title: Molecular mechanism of ethylene stimulation of latex yield in rubber tree (Hevea brasiliensis) revealed by de novo sequencing and transcriptome analysis

status: Public on Feb 23 2016

first: Wankun

last: Deng

state: Not US or Canada

address: Huazhong University of Science and Technology, Wuhan, Hubei, P.R.C.

department: Life Science and Technology

summary:
Purpose: de novo sequencing and comparative analysis of the bark transciptomes of Hevea brasiliensis induced without ethephon (C), with ethephon for 8 hours (E8) and 24 hours (E24) to identify the genes and pathways related to the stimulation of rubber production by ethylene. The goals of this study are to reveal the molecular mechanism behind the stimulation of rubber production by ethylene.
Methods: Bark RNA was extracted using the TRIzol® Reagent (Invitrogen) and two cDNA libraries, H (healthy rubber trees) and T (TPD-affected trees), were prepared using the mRNA-Seq 8 sample prep Kit (Illumina). The libraries were deep sequenced using Illumina HiSeqTM 2000 (Illumina Inc., San Diego, CA, USA). Raw reads produced from sequencing machines were resorted to de novo assembly and gene annotation.
Results: De novo sequencing and assembly of the bark transciptomes of Hevea brasiliensis induced with ethephon for 8 hours (E8) and 24 hours (E24) were performed. 51,965,770, 52,303,714 and 53,177,976 high-quality clean reads from E8, E24 and C (control) samples were assembled into 81,335, 80,048 and 80,800 unigenes respectively, with a total of 84,425 unigenes and an average length of 1,101 bp generated. 10,216 and 9,374 differentially expressed genes (DEGs) in E8 and E24 compared with C were respectively detected. The expression of several enzymes in crucial points of regulation in glycolysis were up-regulated and DEGs were not significantly enriched in isopentenyl diphosphate (IPP) biosynthesis pathway. In addition, up-regulated genes of great regulatory importance in carbon fixation (Calvin cycle) were identified.
Conclusions: The rapid acceleration of glycolytic pathway supplying precursors for the biosynthesis of IPP and natural rubber, instead of rubber biosynthesis per se, may be responsible for ethylene stimulation of latex yield in rubber tree. The elevated rate of flux throughout the Calvin cycle may account for some durability of ethylene-induced stimulation. Our finding lays the foundations for molecular diagnostic and genetic engineering for high-yielding improvement of rubber tree.

overall_design: De novo sequencing of the transcriptomes of C (bark without ethephon application), E8 (bark with 1.5%-ethephon treatment for 8 hours) and E24 (bark with 1.5%-ethephon treatment for 24 hours) rubber trees was conducted using Illumina HiSeq 2000.

first: Jin-Ping

last: Liu

first: Yu-Fen

last: Zhuang


title: Functional genomic responses to temperature variation in adult Drosophila mojavensis

city: Las Vegas

first: Allen

middle: G.

last: Gibbs

state: Nevada

address: 4505 S Maryland Parkway

department: School of Life Sciences

institute: University of Nevada

summary: Investigation of whole genome transcription expression level changes in Drosophila mojavensis wild-type populations (1 Punta Onah: PO, 2 Organ Pipe National Monument: OPNM, 3 Punta Prieta:PP, and 4 San Quintin: SQ). The experiment was designed to investigate functional genomic responses to temperature variation (15, 25, and 35 °C) in adult Drosophila mojavensis wild populations. For each treatment 1-5 replicates were used (R1, R2, R3, R4 & R5). SO and BC represents Sonora deserts and Baja California region respectively.

overall_design: A total of 97 hybridizations were performed in this entire experiment. We used 135K 12-plex NimbleGen arrays. Total RNA was recovered from each sample listed below. The experimental design consisted a total of four populations (Punta Onah:PO; Organ Pipe National Manument:OPNM, Punta Prieta:PP and San Quintin:SQ),  two host diets (Agria:AG and Organ pipe:OP) and three temperature treatments (15, 25 and 35 °C). Each chip measures the expression level of 14528 transcripts. One to 5 replicates were used for each type (R1, R2, R3, R4 and R5). Fly source details are as follows: Punta Onah 2007:PO07; Organ Pipe National Monument 2008:OPNM08; Punta Prieta 2008:PP08; San Quintin 2008:SQ08.

middle: G

first: William

last: Etges

first: Cassia

last: de Oliveira

first: Subhash

last: Rajpurohit


title: Comprehensive Epigenomic Analysis Reveals Dynamic Regulatory Programs Of Blood Development (RNA-seq)

first: MS

last: Vijayabaskar

overall_design: ChIP-seq data of histone modifications and transcription factors, and RNA-seq data obtained from purified cells representing five sequential stages of murine blood cell specification and differentiation. In the expression cufflink file linked at the bottom of the Series record, there is processed data for a HE Sample, extensively used in this study, but has been uploaded previously in Series GSE55310.

first: Debbie

last: Goode

first: Nadine

first: Kiran

last: Batta

first: Mairi

last: Challinor

first: Kirstie

last: Wallace

first: Salam

last: Assi

first: Pierre

last: Cauchy

first: Jane

last: Gilmour

first: Maarten

last: Hoogenkamp

first: David

last: Westhead

first: Georges

last: Lacaud

first: Valerie

last: Kouskoff

first: Berthold

last: Göttgens

first: Constanze

last: Bonifer


title: Genome-wide analysis of alternative splicing during development and drought in Zea mays

status: Public on Feb 04 2016

city: Newark

first: Shawn

last: Thatcher

state: DE

address: 15 Innovation Way

institute: University of Delaware

summary: Analysis of the maize alternative splicing landscape, including transcript discovery and quantification during development and drought

overall_design: Total RNA was isolated from well-watered and drought stressed leaves, ears and tassels of maize plants and used to construct RNA seq libraries

first: Bailin

last: Li


title: Differential DNA methylation in Latino population

city: San Francisco

first: Esteban

last: Burchard

state: CA

institute: University of California, San Francisco (UCSF)

summary: (1) In clinical practice and biomedical research populations are often divided categorically into distinct racial and ethnic groups. In reality, these categories comprise diverse groups with highly heterogeneous histories, cultures, traditions, religions, as well as social and environmental exposures. While the factors captured by these categories contribute to clinical practice and biomedical research, the use of race/ethnicity is widely debated. As a response to this debate, genetic ancestry has been suggested as a complement or alternative to this categorization. However, few studies have examined the effect of genetic ancestry, racial/ethnic identity, and environmental exposures on biological processes. Herein, we examine the contribution of self-identification within ethnicity, genetic ancestry, and environmental exposures on epigenetic modification of DNA methylation, a phenomenon affected by both genetic and environmental factors. We typed over 450,000 variably methylated CpG sites in primary whole blood of 573 individuals of Mexican and Puerto Rican descent who also had high-density genotype data. We found that methylation levels at a large number of CpG sites were significantly associated with ethnicity even when adjusting for genetic ancestry. In addition, we found an enrichment of ethnicity-associated sites amongst loci previously associated with environmental and social exposures. Interestingly, one of the strongest associated sites is driven by the Duffy Null blood type variant, demonstrating a new function of the locus in lymphocytes. Overall, the methylation changes associated with race/ethnicity, driven by both genes and environment, highlight the importance of measuring and accounting for both self-identified race/ethnicity and genetic ancestry in clinical and biomedical studies and the benefits of studying diverse populations.    (2) In epigenome-wide association studies (EWAS), different methylation profiles of distinct cell-types may lead to false discoveries. We introduce ReFACTor, a method based on principal component analysis (PCA) for the correction of cell-type heterogeneity in EWAS. ReFACTor does not require knowledge of the cell counts, and it obtains improved estimates of the cell-type composition, resulting in improved power and control for false positives in EWAS.

overall_design: Bisulphite converted DNA from 573 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip and a complete blood count with automated white blood cell differential was performed by automated flow cytometry for 95 of the samples.


title: Improved ribosome-footprint and mRNA measurements provide insights into dynamics and regulation of yeast translation

status: Public on Feb 10 2016

middle: Eric

last: Weinberg

address: 600 16th Street, GH S572F

institute: University of California, San Francisco

summary: Ribosome-footprint profiling provides genome-wide snapshots of translation, but technical challenges can confound its analysis. Here, we use improved methods to obtain ribosome-footprint profiles and mRNA abundances that more faithfully reflect gene expression in Saccharomyces cerevisiae. Our results support proposals that both the beginning of coding regions and codons matching rare tRNAs are more slowly translated. They also indicate that emergent polypeptides with as few as three basic residues within a 10-residue window tend to slow translation. With the improved mRNA measurements, the variation attributable to translational control in exponentially growing yeast was less than previously reported, and most of this variation could be predicted with a simple model that considered mRNA abundance, upstream open reading frames, cap-proximal structure and nucleotide composition, and lengths of the coding and 5'-untranslated regions. Collectively, our results provide a framework for executing and interpreting ribosome-profiling studies and reveal key features of translational control in yeast.

overall_design: Ribosome-footprint profiling and RNA-seq (total RNA, poly(A) selected, RiboMinus treated, or Ribo-Zero treated) from log-phase S. cerevisiae. The study includes a reanalysis of the two Samples from GSE53313. The reanalyzed data is linked to the Series record.

middle: E

first: Premal

last: Shah

first: Stephen

last: Eichhorn

first: Jeffrey

last: Hussmann

first: Joshua

middle: B

last: Plotkin

last: Bartel


title: DNA methylation profiling of whole blood and reconstructed mixtures of purified leukocytes isolated from human adult blood

status: Public on Feb 12 2016

city: Kansas City

first: Devin

middle: Charles

last: Koestler

state: KS

address: 3901 Rainbow Blvd.

department: Biostatistics

institute: University of Kansas Medical Center

type: Methylation profiling by genome tiling array

summary: Confounding due to cellular heterogeneity represents one of the foremost challenges currently facing Epigenome-Wide Association Studies (EWAS). Statistical methods leveraging the tissue-specificity of DNA methylation for deconvoluting the cellular mixture of heterogeneous biospecimens such as whole blood, offer a promising solution.  However, their performance depends entirely on the library of DNA methylation markers being used as the basis for deconvolution. The objective of this study was to train and validate an algorithm for the identification of optimal DNA methylation libraries for the deconvolution of adult human whole blood.

overall_design: Purified granulocytes, monocytes, CD4T, CD8T, natural killer cells, and B cells from normal human subjects were purchased from AllCells LLC (Emeryville, CA).  DNA extracted from purified leukocyte subtypes were mixed in predetermined proportions to reconstruct two distinct sets of white blood cell (WBC) mixtures, each consisting of six samples. An additional six whole blood (WB) samples from disease-free adult donors with available immune cell profiling data from flow cytometry were purchased from All-Cells LLC and were included in this investigation.  All DNA samples were bisulfite modified using the Zymo EZ DNA Methylation kit (Irvine, CA) and profiled for DNA methylation using the Illumina HumanMethylation450 array platform.

first: Brock

last: Christensen

first: John

last: Wiencke

first: Karl

middle: T

last: Kelsey


title: microRNA profiles in Parkinson’s disease prefrontal cortex

status: Public on Mar 16 2016

city: Boston

first: Adam

last: Labadorf

state: MA

address: 72 East Concord Street E301

department: Neurology

institute: Boston University Medical School

summary:
Objective. The goal of this study was to examine the microRNA (miRNA) profile of Parkinson’s disease (PD) frontal cortex as compared to normal control brain, allowing for the identification of PD specific signatures as well as the study of disease-related phenotypes, such as onset age or dementia
Methods. Small RNA sequence analysis was performed from prefrontal cortex for 29 PD samples and 33 control samples. After sample QC, normalization and batch correction, linear regression was used to identify miRNAs altered in PD, and a PD classifier was developed using weighted voting class prediction. The relationship of miRNA levels to onset age and PD with dementia (PDD) was also characterized in case-only analyses.
Results. 125 miRNAs were differentially expressed in PD at a genome-wide level of significance (FDR q<0.05). A set of 29 miRNAs classified PD from non-diseased brain (93.9% specificity, 96.6% sensitivity). The majority of differentially expressed miRNAs (105/125) showed an ordinal relationship from control, to PD without dementia (PDN), to PDD. Among PD brains, 36 miRNAs classified PDD from PDN (sensitivity =81.2%, specificity =88.9%). Among differentially expressed miRNAs, miR-10b-5p had a positive association with onset age (q=4.7e-2).
Conclusions. Based on cortical miRNA levels, PD brains were accurately classified from non-diseased brains. Additionally, the PDD miRNA profile exhibited a more severe pattern of alteration among those differentially expressed in PD. To evaluate the clinical utility of miRNAs as potential clinical biomarkers, further characterization and testing of brain-related miRNA alterations in peripheral biofluids is justified.

overall_design: 29 Parkinson's disease prefrontal cortex samples analyzed with 33 control samples from Series GSE64977. The adapter sequence from the sample prep TGGAATTCTCGGGTGCCAAGG.

first: Andrew

last: Hoss

first: Richard

middle: H

last: Myers

first: Jeanne

last: Latourelle


title: Expression data from polarized adult human macrophages

status: Public on Feb 01 2016

city: Montreal

first: Luke

middle: Michael

last: Healy

state: Quebec

address: 3801 University Street

department: Neurology and Neurosurgery

institute: Montreal Neurological Institute

summary:
Myeloid cells are prominent cellular constituents of the CNS. Under physiologic conditions, these include microglia within the parenchyma and systemic compartment derived macrophages localized to the perivascular spaces. Defining the relative distribution and functions of microglia versus blood-derived macrophages in the CNS parenchyma under pathologic conditions remains a challenge due to limitations in being able to distinguish these cell types. Approaches to distinguishing microglia and macrophages in experimental models include use of chimeric and parabiotic animals and molecular genetic techniques to selectively differentially label or delete a specific cell type. The current report will compare gene expression of human microglia and macrophages under distinct states of activation or “polarization” and relate these to their roles in tissue injury and protection /repair in the central nervous system (CNS).
We used Affymetrix Human Gene HT 2.0 microarrays to compare whole transcriptomes of microglia and macrophages under defined polarization conditions.

overall_design: Macrophages isolated from adult human peripheral blood of 3 donors were exposed to different polarization conditions: M0 (MSCF), Mtgf (MCSF+TGFβ), M1 (GMCSF+IFNƴ+LPS), M2a (MCSF+IL4+IL13) and M2c (MCSF+IL10+IL4+IL13) over a 7 day period.

first: Gabrielle

last: Perron


title: Expression data from polarized adult human microglia

overall_design: Microglia isolated from the adult human brain of 3 donors were exposed to different polarization conditions: M0 (no cytokine treatment), Mtgf (TGFβ), M1 (GMSCF+IFNy+LPS), M2a (MCSF+IL4+IL13) and M2c (MCSF+IL10+IL4+IL13) over a period of 7 days


title: Gene expression profiles of normal B-cell subsets from sternal bone marrow

status: Public on Feb 09 2016

city: Aalborg

first: Julie

middle: Støve

last: Bødker

address: Sdr. Skovvej 15

department: Department of Heamatology

country: Denmark

institute: Aalborg University Hospital

summary: Mononuclear cells were isolated from the sternal bone marrow and prepared for multiparametric flow cytometry using an optimized and validated protocol. B-cell subsets of PreBI, PreBII, Immature, Naive, Memory and Plasma cells were isolated and a al of 38 gene expression profiles were generated using the HuEx-1_0-st-v2-micro array chip from Affymetrix to characterize the gene expression in the individual subpopulations.

overall_design: Bone marrow tissue was obtained by physical scraping of the medulla from seven patients (homo sapiens) undergoing cardiac surgery. Mononuclear cells were isolated from bone marrow and prepared for multiparametric flow cytometry using an optimized and validated protocol. B-cell subsets of PreBI, PreBII, Immature, Naive, Memory and Plasma cells were isolated and a total of 38 gene expression profiles were generated using the HuEx-1_0-st-v2-micro array chip from Affymetrix .

first: Karen

last: Dybkær

first: Martin

last: Bøgsted

first: Hans

last: Johnsen


title: Comprehensive Epigenomic Analysis Reveals Dynamic Regulatory Programs Of Blood Development

status: Public on Feb 25 2016

first: MS

last: Vijayabaskar

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

overall_design: Refer to individual Series


title: Germline nuclear RNAi in C. elegans represses transgenerational inheritance of heat-induced gene transcriptional activation

city: Piscataway

first: Sam

middle: Guoping

last: Gu

state: New Jersey

address: 604 Allison Road

department: Molecular Biology and Biochemistry

institute: Rutgers University


title: Gene expression profiles of human bronchoalveolar epithelial cells (HBEC) transduced with GFP labeled murine focal adhesion kinase (PMX-Purom-GFP-mFAK) or in combination with SUMO ligase Pias1

status: Public on Feb 02 2016

city: Dallas

first: Jerfiz

middle: D

last: Constanzo

state: Texas

address: 6001 Forest Park Road

department: Hematology Oncology

institute: University of Texas Southwestern Medical Center

summary:
The goal if this project was to determine the cellular pathways affected by FAK protein overexpression downstream of oncogenic KRAS and RHOA in normal lung epithelium. In addition, we aim to characterize the potential downstream modulators of cell growth and migration upon FAK hyperactivation.
We identified pathways in DNA damage, cell growth, apoptosis and cytoskeleton remodeling pertaining to tissue differentiation and carcinogenesis signature respectively.

overall_design: For this study, two duplicate samples were analyzed in triplicate arrays for a total of 6 data poinst per condition. The groups compared were PMX-Purom-GFP-mFAK against  PMX-Purom-GFP-mFAK + PIAs1

first: Pier

last: Scaglioni


title: Cancer-adipoocyte interaction by co-culture of MCF7 and human primary adipocytes

city: Sendai

first: Minako

last: Sakurai

state: Miyagi

address: 2-1 Seiryo-Machi, Aoba-ku

department: School of Medicine

institute: Tohoku University

summary: Examination of an interaction between adipocytes and MCF7 to identify the genes associated with invasion of carcinoma cells into adjescent adipocytes.

overall_design: To identify up-regulated genes by adipocyte-cancer interaction in breast cancer cells, mono-cultured MCF7 was used as control to compare with 3T3-L1 adipocytes co-cultivated MCF-7 for 72 hours in DMEM

first: Yasuhiro

last: Miki

first: Hironobu

last: Sasano


title: Genome-wide analysis of TIAR RNA ligands in mouse macrophages before and after LPS stimulation

status: Public on Feb 05 2016

city: Barcelona

first: Yacine

last: Kharraz

state: Catalunya

address: 88 calle Aiguader

department: DCEXS

institute: University Pompeu Fabra

summary: TIA-1 related protein (TIAR) is a RNA-binding protein involved in several steps of gene expression such RNA splicing and translation. TIAR contains three RNA recognition motifs (RRMs) allowing its interaction with specific sequences localized in the untranslated regions (UTRs) of several mRNAs.  In myeloid cells, TIAR has been shown to bind and regulate the translation and stability of various mRNAs encoding proteins important for the inflammatory response, such as TNFα, Cox-2  or IL-8 . Here, we generated two macrophage-like RAW 264.7 cell lines expressing either a tagged full-length TIAR protein or a RRM2-truncated mutant unable to bind RNA with high affinity . By a combination of RNA-IP and microarray analysis (RIP-chip), we identified mRNAs specifically bound by the full-length protein both in basal conditions and in response to LPS.

overall_design: Microarray hybridization was performed on TIAR-FLAG-associated mRNAs or TIARΔRRM2-FLAG-associated mRNAs in unstimulated and LPS-stimulated RAW264.7 cells. Enrichment of TIAR-FLAG-associated mRNAs and TIARΔRRM2-FLAG-associated mRNAS were normalized to total transcriptome of TIAR-FLAG and TIARΔRRM2-FLAG expressing-RAW264.7 cells respectively. After amplification and labelling, sample pairs were hybridized onto Mouse Exonic Evidence Based Oligonucleotide (MEEBO) arrays containing on average 38784 mouse 70mer oligonucleotide probes (Stanford University, US). Hybridizations were replicated with dye swap.

first: Anne

last: Lefort

first: Frédérick

last: Libert

first: Christopher

last: Mann

first: Cyril

last: Gueydan

first: Veronique

last: Kruys


title: Expression data from polarized adult human microglia and macrophages

first: Luke

last: Healy


title: Gene expression profile of induced expandable cardiovascular progenitor cells derived from mouse fibroblasts

status: Public on Jan 29 2016

first: Gladstone

last: Bioinformatics

address: 1650 Owens St

department: Data Science and Biotechnology

institute: Gladstone Institutes

summary: We developed a strategy to capture cardiovascular progenitor cells during the cardiac reprogramming from mouse fibroblasts and expand these CPCs for a long term in a chemically defined condition.

overall_design: To study the process of cardiac transdifferentiation, we collected cells at different stages of cardiac reprogramming, including initial 2nd MEFs, MEFs at day9 of reprogramming, ieCPCs, and their derivatives after further cardiac differentiation. To learn the characteristics of ieCPCs during their long-term expansion, we collected ieCPCs at both early and late passages.

first: Yu

last: Zhang

last: Cao

first: Sheng

last: Ding


title: Expression analysis of Mycobacterium tuberculosis H37Rv biofilm after treatment with DTT ( Reduced) for 29 hrs

status: Public on Feb 08 2016

city: Chandigarh

first: Ashwani

last: Kumar

state: Chandigarh

address: Sec 39A

department: Molecular Microbiology

institute: CSIR-Institute of Microbial Tech

summary: Expression profile of Mycobacterium tuberculosis H37Rv biofilm as induced by DTT (Reduced) 6mM

overall_design: DTT reduced at 6 mM concentration was added to log phase culture of Mtb H37Rv. After 29 hours RNA was isolated and hybridization was done on microarrays

first: Abhishek

last: Trivedi

first: Parminder

middle: S

last: Mavi

first: Deepak

last: Bhatt


title: Gene expression analysis in the peripheral blood of baboons for early prediction of the later occurring hematological ARS using human Agilent SurePrint G3 Microarrays, v2 (8x60K)

status: Public on Jan 27 2016

city: Munich

first: Michael

last: Abend

state: Bavaria

address: Neuherbergstr. 11

country: Germany

institute: Bundeswehr Institute of Radiobiology

summary: Based on gene expression changes measured in the peripheral blood within the first 2 days after irradiation we aimed to predict the later occurring hematological acute radiation syndrome (HARS). Altogether 18 baboons were irradiated simulating different patterns of partial body irradiation or total body irradiation corresponding to an equivalent dose of 2.5 or 5 Gy. According to changes in blood cell counts (BCC) they were either suffering from H1-2 (n=4) or H2-3 (n=13) degree HARS. One animal was deleted from analysis due to unusual changes in BCC and early death. Blood samples taken before irradiation served as H0 (n=17). A two stage study design was applied. During first stage we screened the whole genome (mRNA microarrays) using one part of the samples (H0 n=5, H1-2 n=4, H2-3 n=5). Candidate genes differentially up- or down-regulated during the first two days after irradiation were forwarded for validation in stage II using the remaining samples and changing the methodology (qRT-PCR). Differential gene expression was defined as a significant (p<0.05) and > 2-fold difference in gene expression over H0. From about 20,000 genes on average 46% appeared expressed. At H2-3 and day 1 about 2-3 times more genes appeared up-regulated (1,418 versus 550) or down-regulated (1,603 versus 735) compared to H1-2 an effect which became pronounced at day 2 while the number of differentially expressed genes decreased. These genes did show an enrichment regarding biological processes coding for immune system processes, natural killer cell activation and immune response (p= 1xE-06 up to 9xE-14). Based on the p-value, the height and constant differential gene expression over time, 89 candidate genes were selected for validation using qRT-PCR. Finally, 22 genes for identification of H1-3 and 7 genes for identification of H2-3 were confirmed using qRT-PCR. For H1-3 most genes were constantly and 3-5 fold down-regulated relative to H0 over both days, but some genes appeared 10.3-fold (VSIG4) or even 30.7-fold up-regulated (CD177) over H0. For H2-3 some genes appeared 4-7-fold up-regulated relative to H0 (RNASE3, DAGLA, ARG2), but other genes showed a strong and 14-33-fold down-regulation relative to H0 (WNT3, POU2AF1, CCR7). Each of the genes allowed an almost complete separation of HARS categories. Taken together, clinical relevant HARS can be independently predicted with each of 29 radiation-induced genes examined in the peripheral blood of baboons within the first two days after irradiation.

overall_design: A two stage study design was applied. During first stage we screened the whole genome (mRNA microarrays) using one part of the samples (H0 n=5, H1-2 n=4, H2-3 n=5). Candidate genes differentially up- or down-regulated during the first two days after irradiation were forwarded for validation in stage II using the remaining samples and changing the methodology (qRT-PCR, n=35). This database contains the Agilent micorarray data only.

first: M

last: Port

first: F

last: Herodin

last: Valente

last: Drouet

first: A

last: Lamkowski

last: Majewski


title: Gene expression profiles of B cells under various conditions

status: Public on Jan 28 2016

city: Shanghai

first: Yuhang

last: Jiang

address: 320 Yueyang Road

department: Institute of Health Sciences

institute: Shanghai Institutes for Biological Sciences, CAS

summary: To validate the functions that iron might play in B cell proliferation and function we used deferoxamine (DFO, a widely used iron chelator) to create an iron-deficient environment for cell culture in vitro.

overall_design: We measured B cell proliferative responses to mitogenic stimuli under several conditions, primary splenic B cells cultured in normal medium, or in the presence of  DFO (deferoxamine, 20uM) ,or DFO accompanied with an additional supplement of FAC (Ferric ammonium citrate, 100uM) or FAC(100uM) alone in the medium, unstimulated or stimulated anti-IgM(10ug/ml) or LPS (2ug/ml) for 48h.


title: Effects of the soluble cytoplasmic tail (D2-domain) of CD45 on human T-cell activation

city: Måløv

first: Klaus Stensgaard

last: Frederiksen

address: Novo Nordisk Park F9.1.07

department: Molecular Genetics

institute: Novo Nordisk A/S

summary: Human peripheral blood T cells (total CD3+) were stimulated for 12 and 24 h with plate bound CD3/CD28 or CD3/CD63 mAbs in the presence or absence of the D2-domain of the cytoplasmic tail of CD45. Total RNA was purified and gene expression profiles were obtained.

overall_design: A total of 8 samples consisting of CD3+ T-cells from healthy volunteers were stimulated for 12 and 24 hours with plate bound CD3/CD28 or CD3/CD63 mAbs in the presence or absence of the D2-domain of the cytoplasmic tail of CD45 (aa942-1226 fused to an Fc-backbone as previously described by Kirchberger et al. in Blood 112(4):1240-1248). Total RNA was isolated from the samples and compared by full transcriptome profiling using Affymetrix HG-U133 plus 2.0 GeneChips.

first: Klaus

first: Alexander

last: Puck

first: Johannes

last: Stöckl


title: Identification of differentially expressed genes related to cytoplasmic male sterility in radish (Raphanus sativus L.) by comparative transcriptome analysis

status: Public on Jan 21 2016

city: Changsha

first: Touming

last: Liu

address: NO.348, western road of xianjia lake

department: Institute of Bast Fiber Crops

institute: Chinese Academy of Agricultural Sciences

summary: Cytoplasmic male sterility (CMS), a typically maternally inherited trait, causes a failure in producing functional pollen. Although the radish CMS has be widely used to produce hybrid varieties in breeding program, the molecular mechanism of CMS in radish is poorly understood. In this study, two radish CMS lines (HYBP-A and YH-A) and their corresponding maintainer lines (HYBP-B and YH-B) were used to identify genes potentially involving in CMS using Illumina pair-end sequencing. A total of 167.86 million clean sequence reads were generated from the eight libraries (two replicates for each line). These reads were eventually assembled into 130,240 unigenes. Of them, 67,173 (51.6%) unigenes were annotated for their function. Comparison of gene expression levels between CMS line and maintainer line revealed 5,893 differentially expressed genes (DEGs) in HYBP, and 3,739 DEGs inYH. There were 990 DEGs commonly identified in both HYBP and YH, with same direction of expression change in two CMS lines relative to their corresponding maintainer lines, which suggested these 990 DEGs is likely related to CMS of radish. The expression levels of 20 DEGs were further confirmed by real-time quantitative PCR (qRT-PCR). Two pathways and eight functional categories exhibited a significant enrichment with DEGs in HYBP, and one pathway and six functional categories were markedly enriched by DEGs in YH. Among these pathways/functional categories, four of them were enriched in both varieties. A series of candidate genes and pathways that may contribute to the CMS will be helpful for increasing our understanding for this trait in radish.

overall_design: Two CMS lines and two their corresponding maintainer lines were used. a total of eight samples, i.e. two replicates for each line were used for RNA-seq.


title: Germline nuclear RNAi in C. elegans represses transgenerational inheritance of heat-induced gene transcriptional activation (sRNA profiling)

first: Sam

last: Gu

summary: Environmental stress-induced transgenerational epigenetic effects have been observed in various model organisms and human. The capacity and mechanism of such phenomena, particularly in animals, are poorly understood. In C. elegans, siRNA mediates transgenerational gene silencing through the germline nuclear RNAi pathway. At the organismal level, this pathway plays a transgenerational role in maintaining the germline immortality when C. elegans is under a mild heat stress. However, the underlying molecular mechanism is unknown. In this study, we performed a 12-generation temperature-shift experiment (15˚C->23˚C->15˚C) using the wild type (N2) and a mutant strain that lacks the germline-specific nuclear AGO protein HRDE-1/WAGO-9. We found that the temperature-sensitive mortal germline (Mrt) phenotype of the hrde-1 mutant is reversible, indicating a transgenerational cumulative but also reversible nature of the underlying molecular cause. By taking the whole-genome RNA and chromatin profiling approaches, we revealed an epigenetic role of HRDE-1 in repressing heat stress-induced transcriptional activation of over 280 genes, predominantly in or near LTR retrotransposons. Strikingly, for some of these elements, the heat stress-induced transcription becomes progressively activated in the hrde-1 mutant over several generations under heat stress. Furthermore, the effect of heat stress-induced transcription activation is heritable for at least two generations after the heat stress. Interestingly, the siRNA expression of these genes tend to be heat-inducible in the wild type animals, but not in the hrde-1 mutant, suggesting a role of siRNAs in repressing heat-inducible elements. Our study revealed a novel phenomenon of transgenerational feed-forward transcriptional activation, which is normally repressed in the wild type C. elegans by the germline nuclear RNAi pathway. It also provides a new paradigm to study epigenetic circuitry that connects the environment and gene regulation in the germline.

overall_design: In this study, we performed a 12-generation temperature-shift experiment (15˚C->23˚C->15˚C) using the wild type and hrde-1 mutant. mRNA-seq, Pol II ChIP-seq, H3K9me3 ChIP-seq, and small RNA-seq analyses were performed for all or some of the generations. The effects of temperature change in whole-genome mRNA expression, siRNA expression, gene transcription, and H3K9me3 were investigated at the multigenerational time scale in both the WT and hrde-1 mutant animals.

first: Julie

middle: Z

last: Ni

first: Natallia

last: Kalinava

first: Esteban

last: Chen

first: Alex

last: Huang

first: Thi

last: Trinh


title: Germline nuclear RNAi in C. elegans represses transgenerational inheritance of heat-induced gene transcriptional activation (mRNA profiling)


title: Germline nuclear RNAi in C. elegans represses transgenerational inheritance of heat-induced gene transcriptional activation (chip-seq analysis)