title: Comparison of gene expression profile of muscle samples stored under vacuum at +4°C up to 14 days from growth promoters-treated and control cows.

first: sara

last: pegolo

summary: A bovine oligo microarray platform (GPL7053) was used to evidence differences in gene expression profiles of muscle samples from five (5) dexamethazone plus estradiol treated cows and from five (5) control animals. Samples were stored under vacuum at +4°C and collected at D0 and D14.

overall_design: In this study, we analyzed twenty (20) bovine neck muscle samples stored under vacuum at 4°C and collected at D0 (10) and D14 (10) from five (5) dexamethazone plus estradiol treated cows and five (5) from control animals. Gene expression profiling was performed using the Agilent-015354 Bos taurus Oligo Microarray platform (GPL7053) based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. Feature Extraction (FE) 9.5 used XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.

first: Sara

last: Pegolo

first: Luca

last: Bargelloni


title: Galectin-9 suppresses growth of hepatocellular carcinoma in vitro

status: Public on Mar 01 2015

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: Galectin-9 suppresses growth of Li-7 cells, a cell line of human hepatocellular carcinoma, in vitro study.

overall_design: Micro RNA expression of Li-7 cells, a cell line of hepatocellular carcinoma, with or without administration of galectin-9 were assessed in vitro.

first: Koji

last: Fujita

first: Tsutomu

last: Masaki


title: Profiling gene expression during root induction in juvenile and mature cuttings of Eucalyptus grandis revealed developmental and auxin dependent regulation of the microtubule system

status: Public on May 01 2015

city: Rishon Le-Zion

first: Ron

last: Ophir

address: Hamacabim St.

department: Fruit Tree Sciences

country: Israel

institute: Agricultural Research Organization - the Volcani Center

summary: Rooting capability is one of the economically traits lost during the juvenile to mature phase change in woody plants. A comprehensive microarray analysis was performed to compare the profiles of gene expression in juvenile and mature cuttings from E. grandis, either auxin treated or untreated on days, 0, 1, 3, 6, 9 and 12 post excision. At the end of the experiment, root primordia were observed only in auxin treated juvenile cuttings. Clustering the expression profiles revealed that the time after excision contributed to expression differences more than the age or auxin. Maximum differences contributed by the age and auxin occurred on day 6 which correlated with the kinetics of root primordia formation. These included genes related to the microtubules (MTs) system. Therefore, expression of 42 transcripts annotated as tubulin or MTs associated proteins (MAPs) was validated in the same RNA samples. The results suggest developmental and auxin regulation of MTs. To determine the relevance to adventitious root (AR) formation, subtle perturbations to MTs were performed with trifluralin during induction. While juvenile cuttings were not affected, improved rooting was obtained in mature cuttings. Taken together it suggests that specific MTs remodeling is required for AR formation in E. grandis.

overall_design: mRNA samlpes from mature and juvenile Eucalyptus sections immediately after cutting served as contorls. The rest of the samples were mature and juvenile sections, treated of not treated with Auxin, 1, 3, 6, 9 and 12 days after the prunning. At each time point, a loop design was performed consisting of a juvenile untreated vs. mature untreated array, a matrue untreated vs. mature auxin treated array, a matrue auxin treated vs. juvenile auxin treated array, and a juvenile auxin treated vs. juvenile untreated array. additional arrays connected between these loops, and between them and the time 0 controls. Most conditions had 3 replicates, but mature-untreated-day1 had 4 replicates, and three conditions had 2 replicates each: Juvenile-auxin-treated-day1, juvenile-untreated-day6, and mature-auxin-treated-day9.

first: Mohamad

last: Abu-Abied

first: David

last: Szwerdszarf

first: Inna

last: Mordehaev

first: Yossi

last: Yaniv

first: Joseph

last: Riov

first: Einat

last: Sadot


title: Comparative expression during feeding against starvation in the rice brown planthopper, Nilaparvata lugens

status: Public on Apr 22 2015

city: Tsukuba

first: Yuki

last: Nakamura

state: Ibaraki

address: 1-2 Owashi

institute: National Institute of Agrobiological Sciences

summary: Nilaparvata lugens, the brown planthopper (BPH) sucks the rice phloem sap containing high sucrose to obtain carbon source. The comparative gene expression analyses were perfomed during feeding against starvation in order to determine sugar transporter and other feeding related gene expression.

platform_organism:
Tetranychus urticae
Nilaparvata lugens

overall_design: Young BPH females that feed rice seedlings or feed-deprived (water-supplied) for 24 hours were prepared in triplicate. Gene expression was compared in these two groups: feeding and feed-deprived.

first: S

last: Kikuta

first: Y

first: H

last: Noda


title: Genome-wide features of neuroendocrine regulation in Drosophila by the basic helix-loop-helix transcription factor DIMMED

status: Public on Feb 02 2015

city: Saint Louis

first: Tarik

last: Hadzic

state: MO

address: 660 S. Euclid Ave

department: Psychiatry

country: USA

institute: Washington University in St Louis School of Medicine

type: Genome binding/occupancy profiling by genome tiling array

summary: Neuroendocrine (NE) cells use large dense core vesicles (LDCVs) to traffic, process, store and secrete neuropeptide hormones through the regulated secretory pathway. The DIMM basic helix-loop-helix transcription factor of Drosophila controls the level of regulated secretory activity in NE cells. To pursue its mechanisms, we have performed two independent genome-wide analyses of DIMM’s activities: (i) in vivo chromatin immunoprecipitation (ChIP) to define genomic sites of DIMM occupancy and (ii) deep sequencing of purified DIMM neurons to characterize their transcriptional profile. By this combined approach, we showed that DIMM binds to conserved E-boxes in enhancers of 212 genes whose expression is enriched in DIMM-expressing NE cells. DIMM binds preferentially to certain E-boxes within first introns of specific gene isoforms. Statistical machine learning revealed that flanking regions of putative DIMM binding sites contribute to its DNA binding specificity. DIMM’s transcriptional repertoire features at least 20 LDCV constituents. In addition, DIMM notably targets the pro-secretory transcription factor, CREB-A, but significantly, DIMM does not target any neuropeptide genes. DIMM therefore prescribes the scale of secretory activity in NE neurons, by a systematic control of the regulated secretory pathway at steps that are both proximal and distal.

overall_design: DIMM::MYC ChIP-chip (c929>DIMM::MYC/tubGAL80ts) and control (c929>tubGAL80ts): 2 replicates each, input and IP samples. Total of 8 arrays

first: Paul

middle: H

last: Taghert


title: Purified touch receptor neurons: expanded polyGlutamine versus control

status: Public on Feb 01 2015

city: Paris

first: Christian

last: Neri

address: 9 quai St Bernard

department: CNRS UMR 8256, Inserm ERL U1164

country: France

institute: Sorbonne Université, CNRS, INSERM

summary: Transcriptional profiling of C.elegans purified touch receptor neuron precursors, comparing cells expressing mutant Huntingtin N-terminal fragment to normal Huntingtin N-terminal fragment, both fused to GFP under mec-3 promoter. As a control the same experiment has been done with comparing cell expressing normal Huntingtin to GFP only. Goal was to determine the specific effect of expanded polyglutamines on gene expression in purified cell population.

overall_design: Three-condition experiment: mutant Huntingtin (128Q) versus normal Huntingtin (19Q), and normal Huntingtin versus GFP only, 3 biological replicates of each. Cells were purified based on GFP fluorescence using a cell sorter.

first: Cendrine

last: Tourette


title: Real-time quantitative PCR analysis of cucumber mitogen activated protein kinase cascade genes under various stress conditions and plant hormone treatments

city: Hang zhou

first: Jie

last: Wang

state: Zhe jiang province

address: Yu hangtang road 388 of West Lake District

department: Horticulture

country: China

institute: Zhejiang university

summary: We used Bio-Rad laboratories, lnc. PCR assay panel to analyze expression levels of MAPK genes under various stress conditions and plant hormone treatments. Cucumber plants of the ‘Jinyan No.4’ cultivar were reared in growth chambers at 28 ± 1 °C with a photoperiod of 16 h light/8 h dark and light intensity of 400 μmol m−2 s−1. Three-week-old seedlings were used for all abiotic and biotic treatments. For heat or cold treatment, the seedlings were subjected to 35 ± 1 °C or 4 ± 1 °C conditions, respectively. The samples for RNA extraction were collected at 0, 1, 2, 4, and 8 h after treatment. For dehydration treatment, the leaves of plants were sampled  at 0,  2, 4, and 6 d after watering stopped. For disease treatment, Pseudoperonospora cubensis (P.cubensis) was used to infect the seedlings, and leaves were collected at 0, 1, 2, and 3 d after infection. For hormone treatments, the seedling leaves were sprayed with 100 mM methyl jasmonate (meJA) or 100 mM abscisic acid (ABA) and then sampled at 0, 1, 2, 4, and 8 h intervals.

overall_design: The experiment was designed to examine the  transcription patterns of 58 MAPK cascade genes in cucumber in response to three different abiotic stresses (cold, heat, and drought), one biotic stress (Pseudoperonospora cubensis) and two (MeJA and ABA) plant hormone treatments.

first: Changtian

last: Pan

first: Lu

last: Gang


title: Male and female mice show significant differences in hepatic transcriptomic response to TCDD

city: Toronto

first: Stephenie

last: Prokopec

state: Ontario

address: 661 University Avenue, Suite 510

country: Canada

institute: Ontario Institute for Cancer Research

summary:
2,3,7,8–tetrachlorodibenzo-p-dixion (TCDD) is the most potent of the dioxin congeners, capable of causing a wide range of toxic effects across numerous animal models. Previous studies have demonstrated that males and females of the same species can display divergent sensitivity phenotypes to TCDD toxicities. Although it is now clear that most TCDD-induced toxic outcomes are mediated by the aryl hydrocarbon receptor (AHR), the mechanism of differential responses to TCDD exposure between sexes remains largely unknown. To investigate the differential sensitivities in male and female mice, we profiled the hepatic transcriptomic responses 4 days following exposure to various amounts of TCDD (125, 250, 500 or 1000 µg/kg) in adult male and female C57BL/6Kuo mice.
Several key findings were revealed by our study. 1) Hepatic transcriptomes varied significantly between the sexes at all doses examined. 2) The liver transcriptome of males was more dysregulated by TCDD than that of females. 3) The alteration of ‘AHR-core’ genes was consistent in magnitude, regardless of sex. 4) A subset of genes demonstrated sex-dependent TCDD-induced transcriptional changes, including Fmo3 and Nr1i3, which were significantly induced in livers of male mice only. In addition, a meta-analysis was performed to contrast transcriptomic profiles of various organisms and tissues following exposure to equitoxic doses of TCDD. Minimal overlap was observed in the differences between TCDD-sensitive or TCDD-resistant models.
Sex-dependent sensitivities to TCDD exposure are associated with a set of sex-specific TCDD-responsive genes. In addition, complex interactions between the aryl hydrocarbon and sex hormone receptors may affect the observable differences in sensitivity phenotypes between the sexes. Further work is necessary to better understand the roles of those genes altered by TCDD in a sex-dependent manner, and their association with changes to sex hormones and receptors.

overall_design: Adult male and female C57BL/6 mice were treated by gavage with one single-dose TCDD (125, 250, 500, or 1000 μg/kg) in corn oil or corn oil vehicle alone. Animals were euthanized at 96 hours after treatment and tissues were harvested. RNA was isolated from hepatic tissue and the transcriptome for each animal assayed on an individual microarray.

first: Jamie

last: Lee

middle: D

first: John

last: Watson

first: Ren

middle: X

last: Sun

first: Raimo

last: Pohjanvirta

middle: C

last: Boutros


title: Transcriptome analysis of Corynebacterium glutamicum in response to furfural presence

status: Public on Jan 01 2015

city: Seoul

first: Han

middle: Min

last: Woo

address: Hwarangno 14-gil 5, Seongbuk-gu

department: Clean Energy Research Center

country: South Korea

institute: Korea Institute of Science and Technology

summary: To understrand the altered global gene expression levels in C. glutamicum wild type in presence of furfural, transcriptome profiling was performed.

overall_design: Transcriptome profiles of the wild type grown in CgXII medium without furfural and with furfural stresses (each 6.5 mM, 13 mM, and 20 mM) were compared by using the samples taken at the OD600 of 6 (for the control and experiments). Each experiment was performed with a duplicate.

first: Hong-Sil

last: Park

first: Youngsoon

last: Um

first: Sang

middle: J

last: Sim

middle: Y

middle: M


title: Early and late changes in gene and miRNA expression after hepatitis B or C infection in human hepatocyte chimeric mice [serum_miRNA]

status: Public on Dec 01 2014

first: Satoshi

last: Kondo

summary: Changes in gene and microRNA expression 10 days and 8 weeks after infection with hepatitis B and C virus and with or without interferon administration was determined in human hepatocyte chimeric mice.

overall_design:
68 immunodeficient human hepatocyte chimeric mice were allocated into 8 experimental groups. 25 mice were infected with HBV, 22 were infected with HCV, and 21 were reserved as controls. 5 HBV-infected mice and 5 HCV-infected mice were sacrificed at 10 days. Half of the remaining mice were injected with interferon prior to sacrifice, and all mice were sacrificed at 8 weeks.

Please note that only 44 serum samples and 51 tissue samples (out of 68 samples) were included in the study due to RNA degradataion and contamination.

first: Kazuaki

last: Chayama


title: Analysis of global transcriptional response of Mycobacterium tuberculosis H37Rv to the natural compound ethyl p-methoxycinnamate

status: Public on Dec 31 2014

city: Trivandrum

first: Ajay

last: Kumar

state: Kerala

address: Thycaud P.O.

department: Molecular Microbiology

country: India

institute: Rajiv Gandhi Centre for Biotechnology

summary: Gene expression profiling analysis was performed after exposing M. tuberculosis H37Rv to EPMC for 24 and 48 hours. Significant changes in expression levels were observed in the genome in response to the drug. Analysis of the data carried out by studying the expression pattern at the level of pathways, indicated that several pathways including amino sugar and nucleotide sugar metabolism, linoleic acid metabolism, fructose and mannose metabolism, galactose metabolism, lysine degradation pathways were significantly upregulated upon exposure to EPMC, while the pathways involved primarily in the mycobacterial cell wall biosynthesis - the mycolic acid biosynthesis and D-alanine metabolism were significantly downregulated

overall_design: M. tuberculosis H37Rv cells were grown to log-phase and then treated with the compound ethyl p-methoxycinnamate. The drug isoniazid was taken as apositive control. The cells were exposed to the compounds for 24 and 48 hours. Cells to which no compound was added acted as untreated control. After the time points, the cells were harvested and RNA was isolated. The RNA was subjetced to microarray. The data was analysed at pathway level and gene ontology level.

first: Lakshmanan

last: Divya

first: Padiadpu

last: Jyothi

first: K

middle: P

last: Suja

first: Jose

last: Leny

first: Mundayoor

last: Sathish

first: Chandra

last: Nagasuma

first: R

middle: K

last: Ajay


title: A time-series transcriptomic changes of  Streptococcus mutans in response to heat stress

status: Public on Oct 01 2014

city: Köln

first: Yulong

last: Niu

state: Nordrhein-Westfalen

address: Carl-von-Linne-Weg 10

department: Plant Microbe Interactions

country: Germany

institute: Max Planck Institute for Plant Breeding Research

summary: Dental caries are closely associated with the virulence of Streptococcus mutans. The virulence expression of S. mutans is linked to its stress adaptation to the changes in the oral environment. In this work we used whole-genome microarrays to profile the dynamic transcriptomic responses of S. mutans during physiological heat stress. In addition, we evaluated the phenotypic changes, including initial biofilm formation, acid production and ATP turnover of S. mutans during heat stress. There were distinct patterns observed in the way that S. mutans responded to heat stress that included 66 transcription factors for the expression of functional genes being differentially expressed. Especially, response regulators of two component systems (TCSs), the repressors of heat shock proteins and regulators involved in sugar transporting and metabolism co-ordinated to enhance the cell’s survival and energy generation against heat stress in S. mutans.

overall_design: S. mutans UA159 whole-genome arrays (8 x 15 K) were obtained from Agilent and included 1997 probes for S. mutans transcripts. We used time series microarrays to detect the dynamic changes of S. mutans under heat stress. For the exposure to heat stress, cultures of S. mutans (OD600nm=0.5) were transferred from 37℃ to a 45℃ water bath, the temperature of each culture was raised to 42℃ in < 4 min. Then the cultures were transferred to a 42℃ water bath for 5 min, 10 min, 15 min, 30 min, 45 min and 60 min. The control was a cell culture grown at 37℃ and collected before transferred to 45℃ water bath.

first: Chengcheng

last: Liu


title: Transcriptome analysis of the rshA mutant

status: Public on Nov 25 2014

city: Kyoto

first: Masayuki

last: Inui

address: 9-2 Kizugawadai, Kizugawa

institute: Research institute of Innovative Technology for the Earth (RITE)

summary: The extracytoplasmic function sigma factor SigH is responsible for heat and oxidative stress response in a biotechnologically -important bacterium Corynebacterium glutamicum. Due to the hierarchical nature of the regulatory network, it has not been possible to fully determine the SigH regulon by previous transcriptome analyses. Here, we determined the direct genome-wide targets of SigH were determined by ChIP-chip analysis using a deletion mutant of rshA, encoding an anti-sigma factor of SigH. Seventy-five SigH-dependent promoters, including 39 new ones, were identified. Firstly, SigH-dependent heat induction was confirmed for several of the new targets, including two genes (ilvD and lipA) encoding Fe-S cluster containing enzymes. Internal SigH-dependent promoters were found in operon-like gene clusters involved in the pentose phosphate pathway, and riboflavin biosynthesis, and Zn uptake. Accordingly, deletion of rshA resulted in hyperproduction of riboflavin probably due to the coordinated upregulation of these genes. A SigH-dependent promoter was also found upstream of znuC1 in the znuA1C1B1 operon encoding an ABC-type transporter for Zn uptake. Overexpression of znuC1B1 by deletion of rshA and by an IPTG-inducible promoter and similarly affected expression of Zn-responsive genes, indicating that SigH-dependent upregulation of part of the operon potentiates Zn uptake. probably through Zn overload, indicating new physiological roles of SigH. Furthermore, reporter assays demonstrated that rshA in the sigH-rshA operon was heat-inducible under the control of an internal SigH-dependent promoters, identified upstream of rshA within the sigH-rshA operon, while the sigH promoter was independent of SigH, suggesting negative autoregulation of SigH activity.  Finally, a SigH-dependent promoter identified and upstream of sigA encoding the primary sigma factor , wereas highly heat-inducible, but much weaker than the known SigA-dependent one.. The promoter upstream of sigH was independent of SigH but showed weak heat-shock response. The known SigA-dependent sigA promoter was much stronger than the SigH-dependent one. Taken together with the fact that SigH also regulates sigB encoding the primary-like sigma factor, Tthese findings uncovered a complicated regulatory network of the sigma factors.

overall_design: Gene expression profile of the wild type at the exponential phase was compared with that of the rshA deletion mutant. Five independent experiments were performed.

first: Koichi

last: Toyoda

first: Haruhiko

last: Teramoto

first: Hideaki

last: Yukawa


title: Chip-chip analysis of C. glutamicum SigH.

type: Genome binding/occupancy profiling by array

overall_design: ChIP-chip analyses using two strains carrying FLAG-tagged sigH in the background of the wild type and rshA deletion mutant at two growth phases (exponential and stationary phases). Biological replicates: 3 replicates for the rshA mutant at each growth phase, 2 replicates for the wild type at each growth phase.


title: Expression levels of mature miRNAs from Huh7 cell treated with ROCK inhibitor

status: Public on Apr 21 2014

summary: We used microarray to determine the miRNA whose expression was changed at 12 hours after Y27632 treatment

overall_design: Two-condition experiment; Huh7 control vs Huh7 treated with Y27632 for 12 hours

first: Takeshi

last: Yoshikawa

first: Motoyuki

last: Otsuka


title: Expression data from 293T cell treated with ROCK inhibitor

first: Satoshi

last: Kondo

summary: We used microarray to determine the genes whose expression was changed at three or six hours after Y27632 treatment.

overall_design: Three-condition experiment; 293T control vs 293T treated with Y27632 for three hours, 293T control vs 293T treated with Y27632 for six hours.


title: Cascade regulation of sweat gland development by Wnt, Eda and Shh pathways

status: Public on Aug 20 2014

city: Baltimore

first: Chang-Yi

last: Cui

state: MD

address: 251 Bayview Blvd Suite 100, 10C222

department: NIA

institute: NIH

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

overall_design: Refer to individual Series


title: Cascade regulation of sweat gland development by Wnt, Eda and Shh pathways [beta-catenin knockout]

summary: Millions of sweat glands required to maintain body temperature develop from embryonic ectoderm by a poorly defined mechanism. We present evidence for temporal cascade regulation of sweat gland development by Wnt, Eda and Shh pathways. The first stage, sweat gland induction, failed completely when Wnt/β-catenin signaling was blocked in skin epithelium, accompanied by sharp downregulation of Wnt, Eda and Shh pathway genes. In a meta-layer of regulation, Wnt antagonist Dkk4 appeared to operate on sweat gland induction in a negative feedback loop: Dkk4 was itself sharply downregulated in β-catenin-ablated mice, whereas its over-expression repressed Wnt target genes and significantly reduced gland numbers. Eda signaling succeeded Wnt, and activated downstream Shh pathway. Thus, in absence of Eda, Wnt pathway was still active and initial sweat gland pre-germs were seen but failed to develop germs, and dwonstream Shh pathway was repressed. When both Wnt and Eda were intact but Shh was ablated, early stage induction and subsequent duct formation occurred normally, but the final stage formation of secretory coil failed. Thus, sweat gland development shows a relay of regulatory steps, initiated by Wnt/β-catenin -- itself modulated by Dkk4 -- with subsequent tandem action of Eda and Shh pathways.

overall_design: Compared expression changes between wild type and skin specific beta-catenin knockout footpads at 3 developmental time points, E15.5, E16.5 and E17.5. Data were duplicated with 2 sets of samples.


title: DNA copy number detection from exome sequencing - Exploiting the off-targets  (Nimblegen)

status: Public on Aug 12 2014

city: Amsterdam

first: Oscar

last: Krijgsman

state: Outside the US or Canada

address: Plesmanlaan 121

department: Molecular Oncology and Immunology

country: Netherlands

institute: Netherlands Cancer Institute

type: Genome variation profiling by genome tiling array

summary:
Current methods for detection of copy number aberrations (CNA) from whole-exome sequencing (WES) data are based on the read counts of the captured exons only. However, accurate CNA determination is complicated by the non-uniform read depth and uneven distribution of exons. Therefore, we developed ENCODER (ENhanced COpy number Detection from Exome Reads), which eludes these problems. By exploiting the ‘off-target’ sequence reads, it allows for creation of robust copy number profiles from WES. The accuracy of ENCODER compares to approaches specifically designed for copy number detection, and outperforms current exon-based WES methods, particularly in samples of low quality.  Current methods for detection of copy number aberrations (CNA) from whole-exome sequencing (WES) data are based on the read counts of the captured exons only. However, accurate CNA determination is complicated by the non-uniform read depth and uneven distribution of exons. Therefore, we developed ENCODER (ENhanced COpy number Detection from Exome Reads), which eludes these problems. By exploiting the ‘off-target’ sequence reads, it allows for creation of robust copy number profiles from WES. The accuracy of ENCODER compares to approaches specifically designed for copy number detection, and outperforms current exon-based WES methods, particularly in samples of low quality.  Current methods for detection of copy number aberrations (CNA) from whole-exome sequencing (WES) data are based on the read counts of the captured exons only. However, accurate CNA determination is complicated by the non-uniform read depth and uneven distribution of exons. Therefore, we developed ENCODER (ENhanced COpy number Detection from Exome Reads), which eludes these problems. By exploiting the ‘off-target’ sequence reads, it allows for creation of robust copy number profiles from WES. The accuracy of ENCODER compares to approaches specifically designed for copy number detection, and outperforms current exon-based WES methods, particularly in samples of low quality.
DNA copy number profiles generated with a new tool, ENCODER, were compared to DNA copy number profiles from SNP6, NimbleGen and low-coverage Whole Genome Sequencing.

overall_design: DNA copy number profiles of mouse squamous cell lung cancer (SCLC) were generated with ENCODER from whole exome sequencing data and compared to results from  the NimbleGen array

first: T

last: Kuilman

first: O


title: Microarray-based ultra-high resolution discovery of genomic deletion mutations

status: Public on Feb 25 2014

city: Oxford

first: Eric

last: Belfield

state: England

address: South Parks Road

department: Plant Sciences

country: United Kingdom

institute: Oxford University

summary: The use of a graduated series of Arabidopsis thaliana genomic deletion mutations (of sizes ranging from 4 bp to ~5 kb) to optimize CGH-based genomic deletion detection

first: Nicholas

last: Harberd


title: Early and late changes in gene and miRNA expression after hepatitis B or C infection in human hepatocyte chimeric mice [tissue_miRNA]

first: Kazuaki

last: Chayama


title: The effects of apigenin on microRNA expression levels

status: Public on Aug 20 2013

summary: The changes of mature microRNA expression levels after apigenin treatment on Huh7 cells were determined.

overall_design: Huh7 cells were treated with 10microM apigenin for 24hr and the changes of global mature microRNA expression levels were determined.

first: M

last: Ohno


title: Frizzled6 deficiency disrupts the differentiation process of nail development

status: Public on Sep 13 2013

summary: Nails protect the soft tissue of the tips of digits in humans. In birds and mammals the equivalent claws are used for purposes including capturing prey, digging, climbing, fighting and maintaining dexterity and balance. The molecular mechanism of nail (and claw) development is largely unknown, but we have recently identified a Wnt receptor gene, Frizzled6 (Fzd6), as mutated in a human autosomal-recessive nail dysplasia. To investigate the action of Fzd6 in claw development at the molecular level, we compared gene expression profiles of digit tips of wild-type and Fzd6-/- mice, and show that Fzd6 regulates the transcription of a striking number of epidermal differentiation-related genes. Sixty-three genes encoding keratins, keratin associated proteins, and transglutaminases and their substrates were significantly down-regulated in the knockout mice. Among them, four hard keratins, Krt86, Krt81, Krt34 and Krt31; two epithelial keratins, Krt6a and Krt6b; and transglutaminase1 were known to be expressed in nails and involved in nail abnormality when dysregulated. Immunohistochemical studies revealed decreased expression of Krt86, Krt6b and involucrin in the epidermal portion of the claw field in the knockout embryos. We further show that Dkk4, a Wnt antagonist, was significantly down-regulated in Fzd6-/- mice along with Wnt, Bmp and Hh family genes; and Dkk4 transgenic mice showed a subtly but appreciably modified claw phenotype. Thus, Fzd6-mediated Wnt signaling likely regulates the overall differentiation process of nail/claw formation.

overall_design: Heterozygous Fzd6+/- mice (kindly provided by Dr. J. Nathans) were crossed to generate Fzd6+/-, Fzd6-/- and wild-type offspring. Timed matings were set up to harvest embryos at E14.5, E16.5 and E18.5. The morning after mating was designated as E0.5. Tails and the digital tips from forelimbs of three wild-type and Fzd6-/- mice from each embryonic time-point were excised, immediately frozen on dry ice, and stored at    80  C freezer until use. Genotyping was done as described previously (15). RNA was extracted using Trizol Reagent (Life technologies). RNA from dissected forelimbs from each embryo of the three time-points was used for microarray analysis.


title: Transcriptome profiling of Bacillus subtilis OKB105 in response to rice seedlings

status: Public on Oct 17 2014

city: hefei

first: Shanshan

last: Xie

state: anhui

address: No.130 changjiang west road

institute: Anhui agricultural university

summary: Plant growth-promoting rhizobacteria (PGPR) are soil beneficial microorganisms that colonize plant roots for nutritional purposes and accordingly benefit plants by increasing plant growth or reducing disease. But it still remains unclear which mechanisms or pathways are involved in the interactions between PGPR and plants. To understand the complex plant-PGPR interactions, the changes in the transcriptome of typical PGPR standard Bacillus subtilis in responding to rice seedlings were analyzed.

overall_design: We compared and anylyzed the transcriptome changes of the bacteria Bacillus subtilis OKB105 in response to rice seedings for 2 h.  Total RNA was extracted and Random priming cDNA synthesis, cDNA fragmentation and terminal labeling with biotinylated GeneChip DNA labeling reagent, and hybridization to the Affymetrix GeneChip Bacillus subtilis Genome Array.

first: X

last: Gao

first: S

first: H

last: Wu

first: L

last: Chen

last: Zhang

first: Y


title: transcriptome and translatome of arabidopsis wt seeds according to dormancy-transcriptomic and translatomic analysis of Arabidopsis seeds

status: Public on Sep 27 2014

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

summary: au13-12_polysome - transcriptome and translatome of arabidopsis wt seeds according to dormancy - Identification of transcripts that are differentially abundant (transcriptome) and transcripts that are addressed to translation (translatome) in imbibed Arabidopsis seeds in relation with dormancy. During imbibition of seeds (16h and 24h in darkness at 25°C, dormant and non-dormant seeds), transcriptome analysis is done on total RNA and translatome analysis on polysomal RNA. - At harvest seeds are dormant. They stay dormant if they are stored at -20°C (D) and become non-dormant (ND) if they are stored 3 weeks at +20°C. Arabidopsis dormant seeds do not germinate at 25°C in darkness while non-dormant seeds do. Total RNA and polysomal RNA (polysomal fractions purified on sucrose gradients) were extracted from imbibed seeds for 16h or 24h at 25°C in darkness (3 biological replicates). Transcriptome and translatome are compared for Dormant vs Non-Dormant for 16h and 24 imbibition. In silico comparison will allow to compare transcriptome and translatome for each point and type of seeds and to compare the time points (16 vs 24h) for each type of sample.

overall_design: 12 dye-swap - time course

first: Sandrine

last: Balzergue

first: Ludivine

last: Taconnat

first: Juliette

last: Leymarie

first: Marie-Laure

last: Martin-Magniette


title: Genome-wide analyses of C. glutamicum SigH

status: Public on Nov 24 2014

first: Masayuki

last: Inui

first: Koichi

last: Toyoda

first: Haruhiko

last: Teramoto

first: Hideaki

last: Yukawa


title: Cascade regulation of sweat gland development by Wnt, Eda and Shh pathways [Dkk4 transgenic]

first: Chang-Yi

last: Cui

summary: Millions of sweat glands required to maintain body temperature develop from embryonic ectoderm by a poorly defined mechanism. We present evidence for temporal cascade regulation of sweat gland development by Wnt, Eda and Shh pathways. The first stage, sweat gland induction, failed completely when Wnt/β-catenin signaling was blocked in skin epithelium, accompanied by sharp downregulation of Wnt, Eda and Shh pathway genes. In a meta-layer of regulation, Wnt antagonist Dkk4 appeared to operate on sweat gland induction in a negative feedback loop: Dkk4 was itself sharply downregulated in β-catenin-ablated mice, whereas its over-expression repressed Wnt target genes and significantly reduced gland numbers. Eda signaling succeeded Wnt, and activated downstream Shh pathway. Thus, in absence of Eda, Wnt pathway was still active and initial sweat gland pre-germs were seen but failed to develop germs, and dwonstream Shh pathway was repressed.  When both Wnt and Eda were intact but Shh was ablated, early stage induction and subsequent duct formation occurred normally, but the final stage formation of secretory coil failed.  Thus, sweat gland development shows a relay of regulatory steps, initiated by Wnt/β-catenin -- itself modulated by Dkk4 -- with subsequent tandem action of Eda and Shh pathways.

overall_design: Compared expression changes between WT and skin specific Dkk4 transgenic footpads at 2 developmental time points, E15.5 and E16.5. Data were duplicated with 2 sets of samples.


title: ß-amylase1 mutant Arabidopsis plants show improved drought tolerance due to reduced starch breakdown in guard cells

status: Public on Jun 30 2015

city: Erlangen

first: Christian

last: Prasch

address: Staudtstrasse 5

department: Biochemistry division

institute: FAU Universität Erlangen-Nürnberg

summary: In plants, drought stress is a major growth limiting factor causing cell water loss through open stomata. In this study, guard cell-specific transcripts from drought-stressed Arabidopsis plants were analyzed and a down-regulation of β-amylase 1 (BAM1) was found. In previous studies, BAM1 was shown to be involved in stomatal starch degradation under ambient conditions. Impaired starch breakdown of bam1 mutant plants was accompanied by decreased stomatal opening. Here, we show that drought tolerance of bam1 mutant plants is improved as compared to wild type controls. Microarray-analysis of stomata-specific transcripts from bam1 mutant plants revealed a significant down-regulation of genes encoding aquaporins, auxin- and ethylene-responsive factors and cell-wall modifying enzymes. This expression pattern suggests that reduced water-uptake and limited cell wall extension are associated with the closed state of stomata of bam1 mutant plants. Together these data suggest that regulation of stomata-specific starch turnover is important for adapting stomata opening to environmental needs and its breeding manipulation may result in drought tolerant crop plants.

overall_design: Stress induced gene expression in Arabidopsis stomata was measured after exposure to single heat stress. Heat stress conditions were analyzed for both Col-0 plants and a T-DNA insertion line for β-amylase 1. Three days before harvesting heat stress was applied (32°C/28°C). Samples were taken by pooling the stomata of six to eight leaves per sample.

first: Uwe

last: Sonnewald


title: Gene expression in Drosophila hemocytes at the onset of metamorphosis, and dependence to the Ecdysone Receptor

status: Public on Oct 25 2013

city: Lisboa

first: Anna

last: Zaidman-Remy

address: Universidade Nova de Lisboa

country: Portugal

institute: CEDOC, Faculdade de Ciências Médicas, FCM, Universidade Nova de Lisboa

summary:
Coupling immunity and development is essential to ensure survival despite changing internal conditions in the organism. The metamorphosis of the fruit fly represents a striking example of drastic and systemic physiological changes that need to be integrated with the innate immune system. However, the mechanisms that coordinate development and immune cell activity in the transition from larva to adult in Drosophila remain to elucidate. The steroid hormone ecdysone is known to act as a key coordinator of metamorphosis. This hormone activates a nuclear receptor, the Ecdysone Receptor (EcR), which acts as a heterodimer with its partner Ultraspiracle (USP). Together, they activate the transcription of primary response genes, which in turn activate the transcription of a battery of late response genes. We have revealed that regulation of macrophage-like cells (hemocytes) by the steroid hormone ecdysone is essential for an effective innate immune response over metamorphosis. We have shown that in response to ecdysone signalling, hemocytes rapidly up regulate actin dynamics, motility and phagocytosis of apoptotic corpses, and acquire the ability to chemotax to damaged epithelia. Most importantly, individuals lacking ecdysone-activated hemocytes are defective in bacterial phagocytosis and are fatally susceptible to infection by bacteria ingested at larval stages, despite the normal systemic production of antimicrobial peptides. This decrease in survival is comparable to the one observed in pupae lacking immune cells altogether, indicating that ecdysone-regulation is essential to hemocyte immune functions and survival after infection.
To better understand the ecdysone regulation of hemocyte activities, we have performed gene expression analysis. In order to identify the genes which expression change at the onset of metamorphosis, we have sorted hemocytes from 3rd instar larvae and from young prepupae and compared their gene expression. Moreover, and in order to identify which genes are regulated by the ecdysone signalling, we have used individuals expressing a dominant negative form of the Ecdysone Receptor specifically in their hemocytes. We have sorted hemocytes from 3rd instar and young prepupae of this genotype to compare their gene expression to the gene expression in larvae and prepupae from the control individuals.

overall_design: Hemocytes were isolated by FACS from selected 3rd instar larvae (at the late feeding stage) and prepupae (from 1h to 2h after puparium formation - APF) corresponding to two different genotypes: individuals w;HmlDeltaGal4, UAS-GFP/+ that express GFP specifically in hemocytes (genotype control), and individuals w;HmlDeltaGal4; UAS-GFP/UAS-EcRB1DN W650A which hemocytes express an Ecdysone Receptor Dominant Negative construct in addition to the GFP (EcRDN). For each of the four conditions we performed three biological replicates.

last: Zaidman-Rémy

first: Antonio

last: Jacinto


title: Gene Expression Analysis of Host Immune Responses in rhesus macaques infected with SIVmac239 or deglycosylated live-attenuated SIV

status: Public on Oct 10 2014

city: Shinjuku

first: Kazuyasu

last: Mori

state: Tokyo

address: 1-23-1 Toyama

department: AIDS Research Center

institute: National Institute of Infectious Diseases

summary: To find the differences in innate immune response between nonpathogenic  and pathogenic SIV infection, we examined transcriptome in PBMCs from macaques infected with pathogenic or nonpathogenic SIV.

overall_design: Juvenile macaques were intavenousy infected with SIVmac239 or ∆5G. Blood samples were collected at 1 week and 3 weeks pi. Total RNA from the PBMCs were used for the microarray analysis. cRNA was hybridized to a rhesus microarray (Agilent ver.2). The data were normalized per chip to the 75 th percentile expression level, then subjected to per gene to normalization to the median expression of uninfected animals.


title: Early and late changes in gene and miRNA expression after hepatitis B or C infection in human hepatocyte chimeric mice

city: Kamakura

first: Satoshi

last: Kondo

address: Tebiro 6-10-1

institute: Toray Industries,Inc.

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

first: Kazuaki

last: Chayama


title: Two-cell developmental block is due to the lack of cytoplasmic lattices in mouse antral oocytes

status: Public on Feb 04 2013

first: Minoru

last: Ko

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

summary: Mammalian oogenesis is a complex mechanism entailing the maturation of primordial follicles into preovulatory follicles followed by the release of antral oocytes. In the ovary, the antral compartment consists of two populations of oocytes whose main difference regards the ability to resume meiosis and to develop, after the egg-sperm fusion, until the blastocyst stage. Still inexplicably, the antral oocytes distinguishable as Surrounded Nucleolus (SN; 70% of the antral oocytes population) are able to develop to the blastocyst stage, while those showing a Not Surrounded Nucleolus (NSN) arrest at the two-cell stage.

overall_design:
RNA labeling and hybridization on microarray was done independently for SN and NSN oocytes with 2 replications. Two sets of 50 antral oocytes were collected in M2 medium and then were labelled with Cy3-CTP. Fluorescently labelled microarray targets were prepared using a Low RNA Input Fluorescent Linear Amplification Kit (Agilent) with 2-round amplification. Cy5-CTP-labeled reference target was produced from mixture of Stratagene Universal Mouse Reference RNA and MC1 cell RNA. Targets were purified using an RNeasy Mini Kit (Qiagen), and then quantified on a NanoDrop scanning spectrophotometer (NanoDrop Technologies). Target cRNA was hybridized to the NIA Mouse 44K Microarray v3.0 (whole genome 60-mer oligo arrays, Agilent Technology, design ID 015087) according to manufacturers protocol (Two-Color Microarray-Based Gene Expression Analysis Protocol, Product # G4140-90050, Version 5.0.1). Slides were scanned with an Agilent DNA Microarray Scanner (model G2505-64120) at 100% and 10% PMT in both channels (except for the two oocyte Samples which were only scanned once each), with a scan resolution of 5um. All hybridizations compared one Cy3-CTP-labeled experimental target to the single Cy5-CTP-labeled reference target which was used for normalization.
In the final analysis, we made a cutoff of 2.0 for the processed data (i.e., if value<2.0, it is set as 2.0) to minimize the noises from 2-round linear amplifications.


title: Systematic discovery of potent cell differentiation-directing transcription factors

status: Public on Mar 14 2014

summary: A network of transcription factors (TFs) determines cell identity, but identity can be altered by overexpressing a combination of TFs. In principle, this opens the possibility of achieving one of the goals of regenerative medicine generating the desired differentiated cells from pluripotent stem cells, such as embryonic stem (ES) cells and induced pluripotent stem (iPS) cells. However, choosing and verifying combinations of TFs for specific cell differentiation has been daunting due to a large number of possible combinations of ~2,000 TFs. Here we report an unbiased systematic approach identifying individual TFs that can direct efficient and rapid specific lineage differentiation. We start from a correlation matrix of global gene expression responses to the induction of single TFs and global gene expression profiles of a variety of tissues and organs. Based on the correlation matrix, we select TFs as examples and show that their overexpression differentiates ES cells into cells of specific organs, as predicted: Sfpi1 for blood cells, Hnf4a or Foxa1 for hepatocytes, and Ascl1 for neurons. Furthermore, we show that transfection of synthetic mRNAs of Sfpi1, Hnf4a, or Ascl1 generate correspondingly specific target cells. These results demonstrate both the wide-ranging utility of this approach to identify potent TFs for cell differentiation, and also the unanticipated capacity of single TFs to directly guide differentiation to specific lineage fates.

overall_design: Previously, we generated the global gene expression profiles obtained by overexpressing single TFs using the NIA mouse ES cell bank, which consists of 137 mouse ES cell lines carrying a doxycycline-regulatable TF. We then generated the correlation matrix by comparing TF-induced gene expression profiles and the expression profiles of a variety of cell types. TFs predicted by the correlation matrix for specific cell differentiation were selected and subjected to the detailed differentiation assays. ES cell lines were cultured in the GMEM with 1% FBS, 10% knockout serum (invitrogen), and LIF (Millipore). To induce differentiation, ES cell lines were cultured in the differentiation medium (DM) [(alpha minimal essential medium, aMEM) supplemented with 10% fetal calf serum and 5 × 10–5 M 2-mercaptoethanol] with or without doxycycline (1 g/ml). The following organ-specific cell culture media were also used: StemPro-34 Serum Free Media (invitrogen) for blood cells, Hepatocyte culture media kit (BD Biosciences) for hepatocytes, and NeuroCult differentiation kit (StemCell Technologies Inc) for neurons.

first: Kohei

last: Yamamizu

first: Alexiei

last: Sharov

first: Yulan

last: Piao

first: Veronika

last: Zsiros

first: Hong

last: Nakazawa

first: David

last: Schlessinger

middle: S


title: Comparison of pear ‘La France’ and its bud mutant ‘Giant Laf’ (2010 expt, receptacle at 1 week before full bloom stage)

status: Public on Dec 31 2012

city: Chikusa-ku

first: Kenji

last: Nashima

state: Nagoya

address: Furo-cho

department: Graduate School of Bioagricultural Sciences

institute: Nagoya University

summary: Bud mutation (bud sport) is mutation occurred in one branch in a tree and the mutant branch shows different phenotype from normal branches. Because bud mutation occurs in a part of plant body, genomic backgrounds of mutant branch and normal branches are the same, except some mutations. Therefore bud mutants are ideal material to identify key genes for important traits of crops. We studied ‘Giant Laf’, a bud mutant setting large fruit, which generated spontaneously in European pear ‘La France’ tree. In ‘Giant Laf’, increase of cell size and DNA reduplication occurred specifically in fruit flesh. The DNA reduplication in ‘Giant Laf’ was observed at 1 week before full bloom stage. This suggested that DNA reduplication observed in ‘Giant Laf’ fruit is not endoreduplication, but endomitosis or nuclear fusion. To identify genes expressed differentially between in ‘Giant Laf’ and in ‘La France’, microarray analysis was performed with RNA from receptacle (fruit flesh) at 1 week before full bloom stage. To isolate the receptacle, laser microdissection was applied. Genes encoding proteins localized in nucleus and cytoskeleton were up-regulated in ‘Giant Laf’. Among these genes, we found several genes which shared homology with previously described DNA reduplication related genes. These are candidates of responsible gene of ‘Giant Laf’ mutation.

overall_design: The gene expression profiles between European pear (Pyrus communis) ‘La France’ and its bud mutant ‘Giant Laf’ were compared. RNA was extracted from receptacle which was isolated from flower bud at 1 week before full bloom stage by using laser microdissection. Three biological replications were analyzed.

first: Hirokazu

last: Takahashi

first: Mikio

last: Nakazono

first: Tokurou

last: Shimizu

first: Chikako

last: Nishitani

first: Toshiya

last: Yamamoto

first: Akihiro

last: Itai

first: Kanji

last: Isuzugawa

first: Toshio

last: Hanada

first: Tadashi

last: Takashina

first: Mari

last: Kato

first: Shogo

last: Matsumoto

first: Akira

last: Oikawa

first: Katsuhiro

last: Shiratake


title: Principal components of embryonic stem cell pluripotency

status: Public on Mar 14 2013

first: Minoru

last: Ko

summary: To decipher gene regulatory networks, we used systematic suppression of 97 transcription factors (TFs) and 7 other genes with shRNA in mouse embryonic stem (ES) cells, followed by global gene expression profiling. Meta-analysis of these data together with the earlier data obtained by the induction of 50 TFs and the existing genome-wide data on TF binding sites identified the sets of regulated target genes for 23 TFs. Principal component analysis shows different roles of two groups of TFs that are active in ES cells: Pou5f1 and Sox2 support the expression of their target genes and prevent the upregulation of trophectoderm-related genes, whereas Esrrb, Sall4, Nanog, Gbx2, Grhl2, Mtf2, Aff1, Tcfap4, and Cdc5l support the expression of targets of Esrrb, including glycolysis genes, and prevent upregulation of targets of Trp53 and Polycomb TFs. If TFs from the second group are downregulated while Pou5f1 and Sox2 are still active, then the cell state changes towards epiblast lineages.

overall_design:
Sequences for shRNA were designed to target 3    untranslated region of genes (Supplementary Table S8). Gene expression change was checked with real time qPCR (Supplementary Figure S7) and Westerm blot. ES cells (ES[MC1R(20)], passage 20) were cultured without feeders and were co-transfected with 1.6  g of shRNA expression vector and 0.4  g of pPyCAG-EGFP-IP carrying expression cassettes for puromycin resistant genes and EGFP using Effectene (Qiagen). Transfected cells were cultured in presence of 1.5  g/ml of puromycin and were harvested at 72 h after transfection. Mock cells were treated with transfection reagent without DNA and cultured in the absence of puromycin. Experiments were done in 3 replications with 2 of them used for gene expression profiling with microarrays.  Total RNA was isolated by TRIzol (Invitrogen) after 2 days. Cy3-CTP labeled sample targets were prepared with total RNA by Low RNA Input Fluorescent Linear  Amplification Kit (Agilent). Cy5-CTP labeled reference target was Stratagene Universal Mouse Reference RNA.

Note that the processed data in the paper, which is also attached as GSE26520_Table_data.txt.gz, is slightly different from the values columns in each sample. The original processed data are normalized with a batch method, as the new batches of arrays added in the set.  The value columns in this submission reflect full normalization as described in the data processing fields in each sample.

last: Nishiyama

first: Alexei

middle: A

last: Sharov

first: Yulan

last: Piao

first: Hien

last: Hoang

first: Bernard

last: Binder

first: Richard

last: Tapnio

first: Justin

last: Malinou

first: Lina

last: Correa-Cerro

last: Yu

first: Li

last: Xin

first: Yuhki

last: Nakatake

first: Carole

last: Stagg

first: Lioudmila

last: Sharova

first: Yong

last: Qian

first: Dawood

last: Dudekula

first: Sarah

last: Sheer

first: Tetsuya

last: Hirata

first: Tomokazu

last: Amano

first: Misa

first: Michal

last: Zalzman

first: Hsih-Te

last: Yang

first: Ilya

last: Goldberg

first: Weidong

last: Wang

first: Ramaiah

last: Nagaraja

first: Michele

last: Evans

first: Dan

middle: L

last: Longo


title: Microarray analysis of deletants of two transcription factor B in the hyperthermophilic archaeon, Thermococcus kodakarensis.

status: Public on Aug 14 2013

city: Sanda

first: Ryota

last: Hidese

state: Hyogo

address: Gakuen 2-1

department: School of Science and Technology

institute: Kwansei-Gakuin University

summary: Thermococcus kodakarensis, which can grow in a wide range of temperatures, from 60°C to 100°C, optimally at 85°C, has two transcription factor Bs, TFB1 and TFB2, both of which are basal transcription factor. TFB1 is unique to hyperthermophiles, but TFB2 is widely conserved in Euryarchaeota. To screen the genes dependent on each TFB in a temperature dependent manner, we investigated the transcriptional profilings of each TFB deletant strain grown at each temperature, 60˚C, 85˚C, and 93˚C, by comparing with the host strain, KU216. Data analyses showed that TFB1 apparently controls the expression of genes essential for motility and adhesion, such as flagellin genes, at  85˚C and 93˚C, but TFB2 regulates genes involved in basal metabolism including amino acid biosynthesis.

overall_design: Two-condition experiment, KU216 vs. DTF1 cells and KU216 vs. DTF2. Technical replicates: 2 DTF1 at 60˚C, 2 DTF1 at 85˚C, 2 DTF1 at 93˚C, 2 DTF2 at 60˚C, 2 DTF2 at 85˚C, 2 DTF2 at 93˚C, independently measured. One replicate per array.

first: Shinsuke

last: Fujiwara

first: Nishikawa

last: Ryo

first: Gao

last: Le

first: Haruyuki

last: Atomi

first: Tamotsu

last: Kanai

first: Masahiro

last: Katano


title: Profile of gene expression in Tax positive (TaxP) cells compared with Tax negative  (TaxN) cells.

status: Public on Jul 27 2012

city: Xinxiang

first: Hui

state: Henan Province

address: eastern section of Jinsui road

department: Research Center for Immunology

institute: Xinxiang Medical University

summary: Investigating the effect of Tax protein on the expression of genes in Jurkat cells. Current study will help us to elucidate the differential gene expression profiles of Tax positive Jurkat cells.

overall_design: The Tax-positive (TaxP) and Tax negative (TaxN) subline of Jurkat were established. mRNA isolated from TaxN or TaxP cell lines were analyzed using gene array.

first: Ying

last: Shi

first: Zhiguo

last: Niu

first: Yun

last: Xia

first: Yan

last: Gao

first: Zhitao


title: Silencing or amplification of endocannabinoid signaling in blastocysts via CB1 compromises trophoblast cell migration

status: Public on Jul 26 2012

first: Minoru

last: Ko

summary: Endocannabinoid signaling plays a key role in multiple events in female reproduction. In this investigation, we discovered an interesting phenomenon that mice with either elevated or silenced endocannabinoid signaling show similar defects in multiple pregnancy events, including preimplantation embryo development. To unravel the underlying mechanisms, microarray studies were was conducted using RNAs collected from WT, Cnr1-/- and Faah-/- mouse blastocysts on day 4 of pregnancy. The results show that about 100 genes showed unidirectional changes under either elevated or silenced endocannabinoid signaling. Analysis of functional grouping of these genes revealed that multiple biological functions and pathways are affected under aberrant endocannabinoid signaling, including cell migration. Several genes from the microarray data were confirmed by quantitative RT-PCR. Cell motility assays validated the predicted compromised cell migration in Cnr1-/- and Faah-/- trophoblast stem cells. This study provides molecular basis for biphasic effects of endocannabinoid signaling in female reproduction

overall_design: To generate Cnr1-/-, Faah-/- and WT embryos, mutant and WT females were mated with males of the same genotypes. On day 4 of pregnancy at 1500h, embryos were collected from oviducts and uteri of pregnant females, because Cnr1-/- and Faah-/- females show aberrant oviductal transport of embryos. As expected, WT embryos were mostly at the blastocyst stage and all of them were collected from uteri. However, Cnr1-/- and Faah-/- females had higher percentages of embryos at the morula stage, and some of them were still in the oviduct. Since gene expression profiles greatly vary depending on the embryonic development stage, morulae were not included in gene expression analysis; only RNAs from blastocysts were used to better understand the effects solely arising from disrupted cannabinoid signaling in blastocysts.

first: Huirong

last: Xie

first: Xiaofei

last: Sun

first: Yulan

last: Piao

first: Anil

middle: G

last: Jegga

first: Stuart

last: Handwerger

first: Sudhansu

last: Dey


title: Apoptosis induction in rat mammary tumor cells by repression of Pla2g4c expression.

status: Public on Apr 19 2012

city: Aomori

first: Naoki

last: Nanashima

state: Aomori

address: 58-1 Mase, Hamadate

department: Department of Nutrition

institute: Aomori University of Health and Welfare

summary: Although some phospholipase A2 forms, the initiator of the arachidonic acid cascade, contribute to carcinogenesis of many organs, the phospholipase A2 group IVc (Pla2g4c) remains to be clarified. When Pla2g4c expression in Rat mammary tumor-1 E4 (RMT-1) cells was knocked down by using specific siRNAs, cell counts were found to decrease to 40 % of the number of control and apoptotic cells were increased. Whole transcript profiling revealed the up-regulation of lipocalin 2 and down-regulation of epithelical marker genes.

overall_design: The expression of Pla2g4c was blocked by transient transfection with Pla2g4c siRNA in RMT-1 cells.

first: Toshiyuki

last: Yamada

first: Shigeki

last: Tsuchida


title: Rejuvenation of pluripotent stem cells by frequent activation of Zscan4, Part B

status: Public on Jun 12 2013

summary: The gold standard for examining pluripotency of stem cells is to see whether cells can contribute to entire body of animals. Here we show that the increased frequency of Zscan4 activation in mouse ES cells not only enhances, but also maintains their developmental potency in long-term cell culture. As the potency increases, even a whole animal can be produced from a single ES cell injected into 4N blastocyst at unusually high success rate. Although Zscan4-activated cells express genes that are also expressed in 2-cell stage mouse embryos, transiently Zscan4-activated state of ES cells is not associated with the high potency of ES cells. It is thus concluded that ES cells acquire higher potency by going through transient Zscan4 activation state more frequently than the regular state. Taken together, our results indicate that frequent activation of Zscan4 can rejuvenate pluripotent stem cells.

overall_design: Previously, we have shown that constitutive and strong expression of Zscan4 arrest the proliferation of ES cells (refs). We sought for the system to mimic the transient expression of Zscan4 and decided to use ERT2 - Tamoxifen-inducible system (refs). The system allows one to keep a transgene off in the absence of Tmx and turn on in the presence of Tmx at will (refs). We first made a plasmid construct pCAG-Zscan4-ERT2, in which ZSCAN4 ORF fused with ERT2 domain can be driven by a strong ubiquitous promoter CAG. To further investigate this, we transfected pCAG-Zscan4-ERT2 plasmid into an F1 hybrid (C57BL/6J vs. 129) ES cell line V6.5 and isolated multiple cell clones. Based on the qRT-PCR analysis of Zscan4 ORF, we found that cell clones showed a variety of Zscan4 expression levels. We selected the clone that showed the highest Zscan4 expression levels (clone #18) and a clone #2 with the background Zscan4 level.

first: Tomokazu

last: Amano

first: Tetsuya

last: Hirata

first: Geppino

last: Falco

first: Manuela

last: Monti

first: Lioudmila

middle: V

last: Sharova

first: Misa

first: Sarah

last: Sheer

first: Hien

last: Hoang


title: FoxA1 regulates sweat secretion through Best2 and Nkcc1 ion transporters

status: Public on Jan 11 2012

first: Minoru

last: Ko

summary: Body temperature is maintained in a narrow range in mammals, primarily controlled by sweating. In humans, the dynamic thermoregulatory organ, comprised of 2-4 million sweat glands distributed over the body, can secrete up to 4 liters of sweat per day1, thereby making it possible to withstand high temperatures and run long distances. The genetic basis for sweat gland function, however, is largely unknown. We find that a forkhead transcription factor, FoxA1, is required to generate mouse sweating capacity. When FoxA1 is ablated, mice are otherwise healthy and sweat gland morphogenesis occurs, but no sweating ensues, with the Nkcc1 sodium/potassium/chloride co-transporter and a specialized Ca2+-activated bicarbonate channel protein, Best2, both sharply down-regulated, and glycoprotein accumulating in gland lumens and ducts. Furthermore, Best2 knockout mice display comparable anhidrosis and glycoprotein accumulation. These findings link earlier observations that both sodium/potassium/chloride exchange and Ca2+ are required for sweat production.  FoxA1 is inferred to regulate two corresponding features of sweat secretion.  One, via Best2, catalyzes a bicarbonate gradient that could help to drive calcium-associated ionic transport; the other, requiring Nkcc1, facilitates monovalent ion exchange into sweat. These mechanistic components can be pharmaceutical targets to defend against hyperthermia and alleviate defective thermoregulation in the elderly2, and may provide a model relevant to more complex secretory processes.

overall_design: For expression profiling of FoxA1, hairless fore footpad skin (6) was collected from FoxA1 knockouts and wild-type littermates at P10, P14 and P31. Three skin samples from 3 embryos for each genotype at each time point were used for biological replicates. Total RNAs were isolated with Trizol (Invitrogen), precipitated by 7.5M LiCl (Ambion), and cyanine-3-labeled cRNAs were hybridized to the NIA Mouse 44K Microarray v3.0  (Agilent Technologies). Triplicate data were analyzed by ANOVA (6). Genes with FDR<0.05, fold difference>1.5 and mean log intensity>2.0 were considered to be significant.

first: Chang-Yi

last: Cui

first: Victoria

last: Childress

first: Marc

last: Michel

first: Adiv

last: Johnson

first: Makoto

last: Kunisada

first: Klaus

last: Kaestner

first: Alan

last: Marmorstein

first: David

last: Schlessinger


title: Zscan4 transiently reactivates early embryonic genes during the generation of induced pluripotent stem cells Part B

status: Public on Jan 06 2012

summary: The generation of induced pluripotent stem cells (iPSCs) by the forced expression of defined transcription factors in somatic cells holds great promise for the future of regenerative medicine. However, due to a poor understanding of the initial reprogramming mechanism, it is difficult to control the efficiency and quality of the iPSCs. Here we show that Zscan4, expressed transiently in 2-cell embryos and embryonic stem cells (ESCs), efficiently produces iPSCs from mouse embryo fibroblasts when coexpressed with Klf4, Oct4, and Sox2. Unlike other factors, Zscan4 is required only for the first few days of iPSC formation. Microarray analysis revealed transient and early induction of preimplantation-specific genes in a Zscan4-dependent manner. Our work indicates that Zscan4 is a previously unidentified potent natural factor that facilitates the reprogramming process through the recapitulation of the early embryonic program.

overall_design: V6.5 ES cells derived from an F1 hybrid strain (C57BL/6 x 129/Sv) were purchased from Thermo Scientific Open Biosystems.  ES cells were cultured at 37C in 5% CO2 in a complete ES medium: DMEM, 15% FBS, 1000 U/ml LIF (ESGRO, Chemicon), 1 mM sodium pyruvate, 0.1 mM non-essential amino acids, 2 mM GlutaMAX, 0.1 mM   -mercaptoethanol, penicillin, and streptomycin. V6.5 ES cells (5x105 cells) in suspension were cotransfected with 2   g of a linearized pCAG-Zscan4-ERT2 vector and 0.4   g of a PL452 vector (Liu et al., 2003) (a neomycin-resistant gene driven by a PGK promoter) using the Effectene (QIAGEN) according to the manufacturer   s protocol, and plated in 100 mm cell culture dishes. After selecting with G418 for 8 days, resulting ES cell colonies were picked, expanded, and frozen. Subsequently, an ES-ZERT cell clone was selected based on the results of genotyping, qPCR, and puromycin-resistance. ES-ZERT cells (10-15 cells) were injected into 2N blastocysts and then transferred to E2.5 recipient females. After genotyping the pups, ZERT chimeric mice carrying pCAG-Zscan4-ERT2 DNA were established.

first: Tomokazu

first: Yuhki

last: Nakatake

first: Yulan

last: Piao


title: Analysis of Arabidopsis transcriptome in response to beta-cyclocitral treatment-Characterization of beta-cyclocitral effects in Arabidopsis thaliana

status: Public on Dec 01 2011

first: Soubigou-Taconnat

last: Ludivine

summary: cea10-03_cyclocitral - analysis of arabidopsis transcriptome in response to b-cyclocitral treatment - Is beta--cyclocitral a bioactive molecule involved in stress response? - Analysis of Arabidopsis transcriptome in response to b-cyclocitral treatment.

overall_design: 3 dye-swap - treated vs untreated comparison

first: Sandrine

last: Balzergue

first: Ludivine

last: Taconnat

first: Fanny

last: Ramel

first: Marie-Laure

last: Martin-Magniette


title: Identification of genes involved in the establishment of plant-microorganism interactions

status: Public on Mar 01 2012

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

summary:
affy_pathogen_medicago - In compatible interaction between plants and biotrophic microorganisms, neoformation of organs occurs to ensure an efficient relationship between both partners. During the interaction between Medicago truncatula and Sinorhizobium meliloti, bacteria induce the development of root nodule with a permanent meristem, and chronically infect plant cells from zone II before differentiating into atmospheric nitrogen fixing bacteroids. M. truncatula is also plant host for root-knot nematodes, such as Meloidogyne incognita. During this compatible pathogenic interaction, root-knot nematodes induce redifferenciation of root cells from the vascular cylinder into specialized feeding cells called “giant cells”. Hyperplasia and hypertrophy of the surrounding cells lead to the formation of typical root galls. This phenomenon invokes host pathways in common with those necessary for nitrogen-nodule formation, suggesting that nematode and rhizobia exploit a relative common strategy of plant cell infection at the cellular and molecular levels. In order to highlight key genes involved in gall and nodule developments, parallel laser microdissection of giant cells from galls and cells from zone II of nodules, followed by transcriptomic analysis, were performed. The RNA pools were extracted from these cells, amplified and used for transcriptomic studies with M. truncatula Affymetrix DNA chips.

Keywords: organ comparison

platform_organism:
Sinorhizobium meliloti
Medicago sativa
Medicago truncatula

overall_design: 12 arrays - Medicago infected with M. incognita or S. meliloti.

first: Didier

last: Hérouart

first: Isabelle

last: Damiani


title: Expression data from aquatic and terrestrial axolotl full thickness epithelial flank wounds collected over seven days

status: Public on Jan 31 2012

city: Gainesville

first: James

middle: R

last: Monaghan

state: FL

address: 2033 Mowry Road

department: Biology

institute: University of Florida

summary: While considerable progress has been made towards understanding the complex processes and pathways that regulate human wound healing, regenerative medicine has been unable to develop therapies that coax the natural wound environment to heal scar-free.  The inability to induce perfect skin regeneration stems partly from our limited understanding of how scar-free healing occurs in a natural setting.  Here we have investigated the wound repair process in adult axolotls and demonstrate that they are capable of perfectly repairing full thickness excisional wounds made on the flank.  In the context of mammalian wound repair, our findings reveal a substantial reduction in hemostasis, reduced neutrophil infiltration and a relatively long delay in production of new extracellular matrix (ECM) during scar-free healing.  Additionally, we test the hypothesis that metamorphosis leads to scarring and instead show that terrestrial axolotls also heal scar-free, albeit at a slower rate.  Analysis of newly forming dermal ECM suggests that low levels of fibronectin and high levels of tenascin-C promote regeneration in lieu of scarring.  Lastly, a genetic analysis during wound healing comparing epidermis between aquatic and terrestrial axolotls suggests that matrix metalloproteinases may regulate the fibrotic response.  Our findings outline a blueprint to understand the cellular and molecular mechanisms coordinating scar-free healing that will be useful towards elucidating new regenerative therapies targeting fibrosis and wound repair.

overall_design: We used microarray analysis to determine the gene expression changes that take place during scar free wound healing in aquatic and terrestrial axolotl salamanders.  Epidermal tissue was harvested using a 4mm biopsy punch.  Two wounds were made along the flank and posterior to the forelimbs. Harvested epidermis was pooled for each animal.  Four biological replicates were collected from uninjured epidermis (D0) and at 1, 3, and 7 days post injury.

first: Ashley

middle: W

last: Seifert

first: S

last: Voss

first: Malcolm

last: Maden


title: Zscan4 transiently reactivates early embryonic genes during the generation of induced pluripotent stem cells

first: Minoru

last: Ko

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

overall_design: Refer to individual Series

first: Tetsuya

last: Hirata

last: Amano

first: Misa

first: Hien

last: Hoang


title: Transcriptional Activation by Oct4 Is Sufficient for the Maintenance and Induction of Pluripotency

status: Public on Feb 27 2012

summary: Oct4 is an essential regulator of embryonic stem (ES) cell pluripotency in vivo and in vitro, as well as a key mediator of the reprogramming of somatic cells to form induced pluriopotent stem (iPS) cells. It is not known whether activation and/or repression of specific genes by Oct4 is relevant to these functions. Here we show that fusion proteins containing the coding sequence of Oct4 or Xlpou91 (the Xenopus homologue of Oct4) fused to activating regions, but not those fused to repressing regions, behave as Oct4, suppressing differentiation and promoting maintenance of undifferentiated phenotypes in vivo and in vitro. An Oct4 activation domain fusion supported ES cell self-renewal in vitro at lower concentrations than required for Oct4 while alleviating the ordinary requirement for the cytokine LIF. At still lower levels of the fusion, LIF-dependence was restored. We conclude that the necessary and sufficient function of Oct4 in promoting pluripotency is to activate specific target genes.

overall_design: Two independent clones from each cell line were used as biological replications. Cy3-CTP-labelled sample targets were prepared from 2.5 μg of total RNA using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent). Cy5-CTP-labelled reference target was produced from 2.5 μg of Stratagene Universal Mouse Reference RNA. Purified target RNA were hybridized to the NIA Mouse 44K Microarray v3.0 (whole genome 60-mer oligo arrays, Agilent Technology, design ID 015087) (Carter et al., 2005) according to the manufacturer's protocol (Two-Colour Microarray-Based Gene Expression Analysis Protocol, Version 5.0.1).  Slides were scanned with an Agilent DNA Microarray Scanner (model G2505-64120) at 100% PMT for the Cy3 channel and 10% PMT for the Cy5 channel with a scan resolution of 5µm. Data was analyzed using NIA Array Analysis (Sharov et al., 2005) using standard statistical conditions (FDR<0.05, 2-fold expression levels change) to unveil genes with changes in expression levels between the samples and controls.

first: Fella

last: Hammachi

first: Gillian

last: Morrison

first: Alessandra

last: Livigni

first: Alexei

last: Sharov

last: O’Malley

first: Keizuke

last: Kaji

first: Santosh

last: Narayan

first: Eirini

last: Papapetrou

first: Mark

last: Ptashne

first: Joshua

last: Brickman


title: Collection of mouse ES cell lines engineered for the forced induction of transcription factors (part B)

status: Public on Nov 10 2011

summary: Here we report the generation of 84 mouse ES cell lines with doxycycline-controllable transcription factors (TFs) which, together with the previous 53 lines, cover 7 - 10% of all TFs encoded in the mouse genome. Global gene expression profiles of all 137 lines after the induction of TFs for 48 hrs can associate each TF with the direction of ES cell differentiation, regulatory pathways, and mouse phonotypes. These cell lines and microarray data provide the building blocks for a variety of future biomedical research applications as a community resource.

overall_design:
This set of data does not use Universal Mouse Reference on Cy5 channel. ES cells  (passage 25) were cultured in the standard LIF+ medium with Dox+ on a gelatin-coated dish through the experiments. Cells from each cell line were split into 6 wells and the media was changed 24 hr after cell plating: 3 wells with Dox+ medium, and 3 wells with Dox- medium to induce transgenic TFs. Dox was removed via washing 3 times with PBS at 3 hours intervals. Total RNA was isolated by TRIzol (Invitrogen) after 48 hr, and two replications were used for real time qPCR (see primers in Supplementary Table S2) and for microarray hybridization. RNA samples were labeled with total RNA by Low RNA Input Fluorescent Linear Amplification Kit (Agilent). For most TFs, we hybridized Cy3-CTP labeled sample from Dox- medium together with Cy5-CTP labeled sample from Dox+ medium. But for 7 TFs we labeled samples from Dox- and Dox+ with Cy3, and hybridized them independently with Cy5-labeled reference target, which is a mixture of Stratagene Universal Mouse Reference RNA and MC1 cells RNA (this method requires a double number of arrays). Analysis showed that both methods produce results of comparable quality.

The arrays are for 2 channel agilent 44K.  We used treated two channels are two separate arrays, and normalized them with an quantile method described in the data processing sections. So we used one supplemental file for two samples (Cy3 and Cy5, or ch1 and ch2).

Supplementary 'processed data' file linked below.


title: Transcriptional profiling of the rat adipose tissue response to TCDD

status: Public on Nov 24 2009

city: Toronto

first: Paul

last: Boutros

address: 101 College Street, Suite 800

institute: Ontario Institute for Cancer Research

summary: Rodents exposed to the environmental contaminant, TCDD, suffer from a number of acute and chronic toxicities, including lethality and a wasting syndrome. Hypothesizing that the wasting syndrome may be caused by changes in adipose tissue -- either in its hormonal regulation or in homeostatic effects -- we profiled the transcriptional response of rat white adipose to TCDD. We employed two separate rat strains: the Long-Evans strain is sensitive to TCDD toxicities while the Han/Wistar strain is over four orders of magnitude more resistant. One day after TCDD exposure few genes were altered in either strain, but after four days a modest number of transcriptional alterations were observed. Strikingly, TCDD had far fewer effects than did a feed-restriction protocol intended to mimic the wasting syndrome itself. Notably several classic TCDD-responsive genes were modulated at all time-points, including Cyp1a1, Cyp1b1, and Nqo1. We therefore concluded that rat adipose tissue is unlikely to be the primary driver of the wasting syndrome, and that another tissue is likely involved.

overall_design: Two strains, each with drug-treated vs. vehicle-control

first: Allan

middle: B

last: Okey

first: Raimo

last: Pohjanvirta


title: Zscan4 transiently reactivates early embryonic genes during the generation of induced pluripotent stem cells  Part A

last: Ko

overall_design:
Secondary MEFs were isolated from E13.5 embryos, which were harvested by tetraploid complementation. Secondary MEFs were plated on gelatin-coated 6-well plates at a density of 1x105 cells/well in the complete ES medium. After 24 h incubation, secondary MEFs were fed with complete ES medium with or without Dox (1.5 μg/ml) and with or without 200 nM Tmx. Culture medium was changed every day. Withdrawal of drugs (Dox or Tmx) was always followed by 1x washing by PBS before changing culture medium.
We cotransfected MEFs with PB-Tet-MKOS and either a PB-Tet-Zscan4 or PB-Tet-DsRed (control). These cells were subsequently cultured in the standard iPSC generation condition (Dox+). Unexpectedly, we found that MEFs transfected with a PB-Tet-Zscan4 show consistently higher efficiency of iPSC generation than MEFs transfected with a PB-Tet-DsRed (control). All selected iPSCs expressed pluripotent marker genes according to RT-PCR analysis and were positive for ALP, Nanog, and SSEA-1. These iPSCs also formed embryoid bodies in hanging drops without LIF and could be differentiated in vitro to cells of all three germ layers. We are currently studying whether the presence of Zscan4 has the beneficial effects on iPSCs in terms of genome stability.

first: Tomokazu

first: Yuhki

last: Nakatake

first: Yulan

last: Piao


title: Dkk4 and Eda regulate distinctive developmental mechanisms for subtypes of mouse hair-2

status: Public on Sep 03 2010

first: Minoru

summary:
Dkk4 transgenic mice in Tabby background lack hair follicle formation. Gene expression profiling showed significant down regulation of Shh pathway genes at E16.5 and E17.5, the secondary hair follicle induction stages.

Keywords: development or differentiation design,genetic modification design

overall_design: To define target genes of Dkk4 during secondary hair follicle induction, we  carried out microarray experiments with mouse back skin samples that from 2  developmental time points including E16.5 and E17.5 of Tabby and Tabby background Dkk4 transgenic mice.

first: Changyi

last: Cui

first: M.

last: Kunisada M

first: Y.

first: V.

last: Childress

first: D.

last: Schlessinger


title: Collection of mouse ES cell lines engineered for the forced induction of transcription factors (part A)

overall_design: This set of data uses Universal Mouse Reference on the Cy5 channel. ES cells (passage 25) were cultured in the standard LIF+ medium with Dox+ on a gelatin-coated dish through the experiments. Cells from each cell line were split into 6 wells and the media was changed 24 hr after cell plating: 3 wells with Dox+ medium, and 3 wells with Dox- medium to induce transgenic TFs. Dox was removed via washing 3 times with PBS at 3 hour intervals. Total RNA was isolated by TRIzol (Invitrogen) after 48 hr, and two replications were used for real time qPCR and for microarray hybridization. RNA samples were labeled using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent). For most TFs, we hybridized a Cy3-CTP labeled sample from Dox- medium together with a Cy5-CTP labeled sample from Dox+ medium. But for 7 TFs, we labeled samples from Dox- and Dox+ with Cy3, and hybridized them independently with a Cy5-labeled reference target, which is a mixture of Stratagene Universal Mouse Reference RNA and MC1 cells RNA (this method requires a double number of arrays). Analysis showed that both methods produce results of comparable quality.


title: Collection of mouse ES cell lines engineered for the forced induction of transcription factors


title: Dkk4 and Eda regulate distinctive developmental mechanisms for subtypes of mouse hair

first: Chang-Yi

first: Makoto

last: Kunisada

first: Victoria

first: David


title: response of ein3eil1 mutants to fe deficiency-Role of ethylene in Fe deficieny response signalling

status: Public on Dec 31 2011

city: Evry

first: Eddy

last: Blondet

address: 2 rue Gaston crémieux

summary: au10-14_fer - response of ein3eil1 mutants to fe deficiency - Response of ein3eil1 mutants to Fe deficiency - Wild type seedlings and ethylene insensitive ein3eil1 seedlings were germinated and grown in the presence of 50 µM Fe or absence of Fe (0 µM) on Hoagland medium agar plates until the age of 6 days. Under these growth conditions symptoms of Fe deficiency develop in the 0 Fe plants. Ethylene is known to promote Fe acquisition responses. Whole seedlings were harvested for transcriptome analysis, in a total of three biological replicates.

overall_design: 12 dye-swap - gene knock out,treated vs untreated comparison

first: Pascal

last: Genschik

first: Sandrine

last: Balzergue

first: Thomas

last: Potuschak

first: Petra

last: Bauer

first: Marie-Laure

last: Martin-Magniette


title: Responsiveness of genes to manipulation of transcription factors in ES cells is associated with chromatin structure and tissue specificity

status: Public on Feb 14 2011

city: Baltimore

summary:
Background: In addition to determining static states of gene expression (high vs. low), it is important to characterize their dynamic status. For example, genes with H3K27me3 chromatin marks are not only suppressed but also poised for activation. However, the responsiveness of genes to perturbations has never been studied systematically. To distinguish gene responses to specific factors from responsiveness in general, it is necessary to analyze gene expression profiles of cells responding to a large variety of disturbances, and such databases did not exist before.
Results: We estimated the responsiveness of all genes in mouse ES cells using our recently published database on expression change after controlled induction of 53 transcription factors (TFs) and other genes.
Responsive genes (/N/ = 4746), which were readily upregulated or downregulated depending on the kind of perturbation, mostly have regulatory functions and a propensity to become tissue-specific upon differentiation. Tissue-specific expression was evaluated on the basis of published (GNF) and our new data for 15 organs and tissues.
Non-responsive genes (/N/ = 9562), which did not change their expression much following any perturbation, were enriched in housekeeping functions. We found that TF-responsiveness in ES cells is the best predictor known for tissue-specificity in gene expression. Among genes with CpG islands, high responsiveness is strongly associated with
H3K27me3 chromatin marks, and low responsiveness is associated with
H3K36me3 chromatin, binding of E2F1, and GABP binding motifs in promoters.
Conclusions: We thus propose the responsiveness of expression to perturbations as a new way to define the dynamic status of genes, which brings new insights into mechanisms of regulation of gene expression and tissue specificity.

This SuperSeries is composed of the SubSeries listed below.


title: Rejuvenation of pluripotent stem cells by frequent activation of Zscan4

first: Tomokazu

last: Amano

first: Tetsuya

last: Hirata

first: Geppino

last: Falco

first: Manuela

last: Monti

first: Lioudmila

last: Sharova

first: Misa

first: Sarah

last: Sheer

first: Hien

last: Hoang


title: B-type lamins differentially associate with specific genes during differentiation without directly affecting their expression

status: Public on Oct 31 2011

first: Minoru

last: Ko

summary: B-type lamins, the major structural component of the nuclear lamina, is thought to play a repressive role in the expression of many of its bound genes whose silencing are known to be critical for cell differentiation during early development.  Using global mapping of lamin-B-chromatin interaction, we find that the binding to lamin-B indeed correlated with gene silencing in mouse embryonic stem cells (ESC) and ESC-derived trophectoderm (TE) lineage cells.  To address whether lamin-B directly suppresses the expression of the bound genes, we have derived ESCs from lamin-B-null mouse blastocysts.  Unexpectedly, microarray analyses of ESCs and TE cells show that B-type lamins do not repress the expression of their bound genes.  Furthermore, the knockout mice that do not express any B-type lamins can develop to term but exhibit small body size and perinatal lethality.  Our studies demonstrate that B-type lamins are not required for cell differentiation during early embryonic development.  Instead, they are required for proper late embryonic and perinatal development.  The availability of the null ESCs and mice opens the door to further define the functions of B-type lamins.

overall_design:
The Dam and Dam-lamin B1 (Lmnb1) lentivirus generated from 293T cells were concentrated by spinning at 25,000 rpm with the SW28Ti rotor (Beckman) for 3 hours. The viral pellets were resuspended in 1x PBS. For ESCs, freshly trypsinized ESCs were plated into a 6-well plate with 2 ml complete GMEM medium containing either Dam or Dam-Lmnb1 lentivirus, spin-infected at 700g for 45 min, and incubated for a total of 48 hours. For TE cells, TSCs were differentiated toward TE cells for 6 days. On day 6, the TE cells were transduced by spin-infection as above with a fresh TS medium containing either Dam or Dam-Lmnb1 lentivirus. The TE cells were incubated for 48 hours after viral transduction.

The adenine-methylated DNAs were amplified from the genomic DNA by adaptor-mediated PCR. The amplified DNAs were labeled by the Dual color DNA labeling kit (Roche). The labeled DNAs were hybridized with 2.1M mouse whole-genome tiling arrays (NimbleGen, 05327911001), which covers non-repetitive regions in approximately 250 bp intervals, according to the manufacturer's recommendation.

This submission represents the gene expression component of the study.

first: Youngjo

last: Kim

first: Alexei

last: Sharov

first: Katie

last: Mcdole

first: Haiping

last: Hao

first: Yixian

last: Zheng


title: Responsiveness of genes to manipulation of transcription factors in ES cells is associated with histone modifications and tissue specificity (2 of 2)

status: Public on Feb 11 2011

summary:
BACKGROUND: In addition to determining static states of gene expression (high vs. low), it is important to characterize their dynamic status. For example, genes with H3K27me3 chromatin marks are not only suppressed but also poised for activation. However, the responsiveness of genes to perturbations has never been studied systematically. To distinguish gene responses to specific factors from responsiveness in general, it is necessary to analyze gene expression profiles of cells responding to a large variety of disturbances, and such databases did not exist before.

RESULTS: We estimated the responsiveness of all genes in mouse ES cells using our recently published database on expression change after controlled induction of 53 transcription factors (TFs) and other genes. Responsive genes (N = 4746), which were readily upregulated or downregulated depending on the kind of perturbation, mostly have regulatory functions and a propensity to become tissue-specific upon differentiation. Tissue-specific expression was evaluated on the basis of published (GNF) and our new data for 15 organs and tissues. Non-responsive genes (N = 9562), which did not change their expression much following any perturbation, were enriched in housekeeping functions. We found that TF-responsiveness in ES cells is the best predictor known for tissue-specificity in gene expression. Among genes with CpG islands, high responsiveness is associated with H3K27me3 chromatin marks, and low responsiveness is associated with H3K36me3 chromatin, stronger tri-methylation of H3K4, binding of E2F1, and GABP binding motifs in promoters.

CONCLUSIONS: We thus propose the responsiveness of expression to perturbations as a new way to define the dynamic status of genes, which brings new insights into mechanisms of regulation of gene expression and tissue specificity

Inhibitors of cell signaling are known to support the pluripotent state of embryonic stem cells (Ying et al. 2008, Nature 453, 519-523, PMID: 18497825). To characterize the effect of inhibitors on the gene expression we treated B6R(5) mouse ES cells (C57BL/6 strain) with FGFR inhibitor PD173074 (100 uM), MEK inhibitor PD98059 (25 uM),and GSK-3 inhibitor BIO (2 uM) 24 hr after plating. Cells were grown without feeders on gelatin coated, 6-well plates, 100,000 cells/well (10^4 cells/cm2), in complete ES medium at 37 0C; 5% CO2. Medium was changed daily. Inhibitors dissolved in DMSO were added 24 hr after plating and cells were harvested 48 hr after treatment (72 hr after plating).  Control cells were treated with DMSO.

Keywords: cell type comparison design,reference design

overall_design: Total RNA was isolated by TRIzol (Invitrogen) after 2 days. Cy3-CTP labeled sample targets were prepared with total RNA by Low RNA Input Fluorescent Linear  Amplification Kit (Agilent). Cy5-CTP labeled reference target was Stratagene Universal Mouse Reference RNA.

first: Akira

last: Nishiyama

first: Yulan

last: Piao

first: Lina

last: Correa-Cerro

first: Marshall

last: Thomas

first: Samir

last: Mehta


title: Dkk4 and Eda regulate distinctive developmental mechanisms for subtypes of mouse hair-1

summary:
Dkk4 transgenic mice in wild-type background showed abnormal hair subtype formation. Gene expression profiling showed significant down regulation of hair follicle-related keratin genes and hair keratin-associated protein genes at E18.5 and P1.

Keywords: development or differentiation design,genetic modification design

overall_design: To define target genes of Dkk4 during hair follicle development, we  carried out microarray experiments with mouse back skin samples that from 4  developmental time points including E14.5, E16.5, E18.5 and P1 of wild-type and wild-type background Dkk4 transgenic mice.

first: Changyi

last: Cui

first: M.

last: Kunisada M

first: Y.

first: V.

last: Childress

first: D.

last: Schlessinger


title: Requirement for Shh and Fox family genes at different stages in sweat gland development (P5)

status: Public on Feb 20 2009

first: Chang-Yi

address: 251 Bayview Blvd Suite 100, 10C222

summary:
Sweat glands play a fundamental role in thermal regulation in man, but the molecular mechanism of their development remains unknown. To initiate analyses, we compared the model of Eda mutant Tabby mice, in which sweat glands were not formed, to wild-type mice.  We inferred developmental stages and critical genes based on observations at 7 time points spanning embryonic, postnatal and adult life. In wild-type footpads, sweat gland germs were detected at E17.5. The coiling of secretory portions started at postnatal day 1 (P1), and sweat gland formation was essentially complete by P5. Consistent with a controlled morphological progression, expression profiling revealed stage-specific gene expression changes. Similar to the development of hair follicles     the other major skin appendage controlled by EDA     sweat gland induction and initial progression was accompanied by Eda-dependent up-regulation of the Shh pathway. During the further development of sweat gland secretory portions, Foxa1 and Foxi1, not at all expressed in hair follicles, were progressively up-regulated in wild-type but not in Tabby footpads. Upon completion of wild-type development, Shh declined to Tabby levels, but Fox family genes remained at elevated levels in mature sweat glands. The results provide a framework for the further analysis of phased downstream regulation of gene action, possibly by a signaling cascade, in response to Eda.

Keywords: cell type comparison design,development or differentiation design

overall_design: To define target genes of Eda during sweat gland development, we  carried out microarray experiments with mouse footpads that from 7  developmental time points including E15.5, E16.5, E17.5, P1, P3, P5 and  8 weeks of wild-type and Tabby mice. This dataset is P5.

first: Makoto

last: Kunisada

first: David


title: Requirement for Shh and Fox family genes at different stages in sweat gland development (P1)

overall_design: To define target genes of Eda during sweat gland development, we  carried out microarray experiments with mouse footpads that from 7  developmental time points including E15.5, E16.5, E17.5, P1, P3, P5 and  8 weeks of wild-type and Tabby mice. This dataset is P1.

first: Minoru


title: Requirement for Shh and Fox family genes at different stages in sweat gland development (Adult)

overall_design: To define target genes of Eda during sweat gland development, we  carried out microarray experiments with mouse footpads that from 7  developmental time points including E15.5, E16.5, E17.5, P1, P3, P5 and  8 weeks of wild-type and Tabby mice. This dataset is Adult data.


title: Requirement for Shh and Fox family genes at different stages in sweat gland development (P3)

overall_design: To define target genes of Eda during sweat gland development, we  carried out microarray experiments with mouse footpads that from 7  developmental time points including E15.5, E16.5, E17.5, P1, P3, P5 and  8 weeks of wild-type and Tabby mice. This dataset is P3.


title: Requirement for Shh and Fox family genes at different stages in sweat gland development

summary:
Sweat glands play a fundamental role in thermal regulation in man, but the molecular mechanism of their development remains unknown. To initiate analyses, we compared the model of Eda mutant Tabby mice, in which sweat glands were not formed, to wild-type mice.  We inferred developmental stages and critical genes based on observations at 7 time points spanning embryonic, postnatal and adult life. In wild-type footpads, sweat gland germs were detected at E17.5. The coiling of secretory portions started at postnatal day 1 (P1), and sweat gland formation was essentially complete by P5. Consistent with a controlled morphological progression, expression profiling revealed stage-specific gene expression changes. Similar to the development of hair follicles     the other major skin appendage controlled by EDA     sweat gland induction and initial progression was accompanied by Eda-dependent up-regulation of the Shh pathway. During the further development of sweat gland secretory portions, Foxa1 and Foxi1, not at all expressed in hair follicles, were progressively up-regulated in wild-type but not in Tabby footpads. Upon completion of wild-type development, Shh declined to Tabby levels, but Fox family genes remained at elevated levels in mature sweat glands. The results provide a framework for the further analysis of phased downstream regulation of gene action, possibly by a signaling cascade, in response to Eda.

This SuperSeries is composed of the SubSeries listed below.

overall_design:
To define target genes of Eda during sweat gland development, we  carried out microarray experiments with mouse footpads that from 7  developmental time points including E15.5, E16.5, E17.5, P1, P3, P5 and  8 weeks of wild-type and Tabby mice.
Refer to individual Series


title: Requirement for Shh and Fox family genes at different stages in sweat gland development (E17.5)

overall_design: To define target genes of Eda during sweat gland development, we  carried out microarray experiments with mouse footpads that from 7  developmental time points including E15.5, E16.5, E17.5, P1, P3, P5 and  8 weeks of wild-type and Tabby mice. This dataset is E17.5.


status: Public on Apr 11 2008

city: Chicago

first: Justin

last: Borevitz

state: IL

department: Ecology and Evolution

institute: University of Chicago

type: Expression profiling by genome tiling array

summary:
Gene expression of Col, Van and reciprocal hybrids using double-stranded cDNA followed by bioprime random labeling, and hybridization to AtTILE1 forward array.
Study on gene expression polymorphism between arabidopsis thaliana accessions Col-0 and Van-0. Study on the inheritance of gene expression in reciprocal hybrids.
Keywords: cDNA hybridization

overall_design: Each genotype has four replicates, Single chanel. Total four genotypes (Col, Van, Col female x Van male, Van female x Col male). Total 16 samples.

first: Xu

last: Zhang

middle: O


title: flg22 treatment & mutants-Gene profiling upon biotic stress treatment. Gene profiling in microRNA mutants.

status: Public on Jun 02 2008

first: Soubigou-Taconnat

last: Ludivine

summary:
rs06-06_mirna - flg22 treatment & mutants - Time course : What are the genes (incuding microRNA precursors) that are differentially regulated upon flg22 treatment? miRNA : What are the genes (including miRNA precursors) that are differentially regulated in a set of microRNA mutants? siRNA : What are the genes (including miRNA precursors) that are differentially regulated in a set of siRNA mutants? - What are the genes (incuding microRNA precursors) that are differentially regulated upon flg22 treatment? 14-day old seedlings treated with flg22 (flagellin- derived peptide).
Keywords: time course,total transcriptome knowledge

overall_design: 7 dye-swap - CATMA arrays

first: Ludivine

last: Taconnat

first: Jean-Pierre

last: Renou

first: Lionel

last: Navarro

first: Marie-Laure

last: Martin-Magniette