title: Effects of early postnatal overnutrition on the hypothalamic DNA methylation pattern

summary: Investigate the persistent effects of early postnatal overnutrition on the developmental establishment of the DNA methylation in the mouse hypothalamus.

overall_design: Early postnatal overnutrition was induced in mice by reducing the litter size from normally 9 (C) to 4 (SL) pups per litter. Hypothalami were collected from both C and SL mice at the age of postnatal day 180 (P180). Genome-wide DNA methylation difference between SL and C were detected by MSAM. Equal amount of genomic DNA from 5 hypothalami of the same group were pooled as one MSAM sample. Two pooled DNA samples for each group were used for comparison that meant total 10 hypothalami for each group. 500ng pooled DNA was serially digested with SmaI and XmaI followed by adaptor ligation and PCR amplification. Two cohybridizations were performed to compare DNA methylation between SL and C hypothalami, with day swap.

first: Ge

last: Li

last: Kohorst


title: Genes differentially expressed Haloferax mediterranei strains: control wild-type strain vs ΔphaEC strain

status: Public on Apr 20 2012

city: Beijing

first: Jing

last: Han

address: NO.1 West Beichen Road, Chaoyang District

country: China

institute: Institute of Microbiology, Chinese Academy of Sciences

summary: Transcriptional profiling of Haloferax mediterranei comparing control wild-type strain with ΔphaEC strain, in which PHA synthase genes are knockouted. ΔphaEC strain is deficient in PHBV accumulation. Goal was to explore the PHBV biosynthetic pathway and to determine their impact on primary metabolism in H. mediterranei.

overall_design: Total RNA from the control Haloferax mediterranei and its ΔphaEC strain were used to generate target cDNA, and then hybridized to 8*15K Haloferax mediterranei genome array genechips, representing about 3800 genes.


title: Digital transcriptome analysis of genes on sex chromosomes in papaya (Carica papaya)

status: Public on Jul 16 2012

city: Ueda

first: Hideo

last: Matsumura

state: Nagano

address: Tokita 3-15-1

department: Gene Research Center

country: Japan

institute: Shinshu University

type: Expression profiling by high throughput sequencing

summary: For identifying genes for sex determination in papaya, digital gene expression analysis by Ht-SuperSAGE (Matsumura et al., 2010) was carried out in flowers from male, female and hermaphrodite plants of papaya.  Total more than 9,273,744 26bp-tags were obtained by sequence analysis using SOLiD3 and mapped on papaya primitive sex chromosome sequences.

overall_design: 6 samples examined: male young flowerbud, male mature flower bud, female young flower bud, female mature flower bud, hermaphrodite young flower bud, hermaphrodite mature flower bud

first: Naoya

last: Urasaki

first: Kazuhiko

last: Tarora

first: Ayano

last: Shudo

first: Hiroki

last: Ueno

first: Moritoshi

last: Tamaki

first: Norimichi

last: Miyagi

first: Kentaro

last: Yoshida

first: Shinichi

last: Adaniya


title: Comparison of the transcriptional profiles of intermediately vancomycin resistant and susceptible S. aureus strains

status: Public on Mar 12 2013

city: Bonn

first: Peter

last: Sass

state: NRW

address: Sigmund-Freud-Straße 25

department: Institute for Microbiology (IMMIP)

country: Germany

institute: University of Bonn

summary:
The phenotype “intermediate vancomycin resistance” in Staphylococcus aureus (CLSI: MIC = 4-8 mg/L) has been assigned to changes that lead to alterations in cell wall synthesis and morphology. Most vancomycin intermediately resistant S. aureus (VISA) strains are characterised by an increased cell wall thickness as a consequence of an activated cell wall biosynthesis and decreased autolysis. The purpose of this study was to analyse the genetic basis of the vancomycin resistance mechanism of the clinical VISA isolate SA137/93A and its spontaneous mutant strain SA137/93G. The methicillin-resistant S. aureus (MRSA) SA137/93A was isolated from a tracheal secretion and displays heterogeneous intermediate vancomycin resistance (hVISA strain, MIC: 8 mg/L in BHI). Subculturing in presence of 6 mg/L vancomycin generated a mutant with homogeneous intermediate vancomycin resistance, that showed an MIC value of 16 mg/L in BHI and was designated SA137/93G. PFGE profiles and phage typing of the strains showed that they were members of the Iberian clone (ST247), which was prevalent in Germany in the early nineties under the designation “Northern German epidemic strain”. Both strains possess a thickened cell wall. However, the vancomycin resistance of strain SA137/93A is most probably enhanced by an increased amount of free D-Ala-D-Ala termini in the cell wall, which is due to decreased crosslinking, whereas the mutant strain SA137/93G shows normal crosslinking. Moreover, strain SA137/93A displays an increased expression of the essential two-component system yycFGHI as a consequence of an IS256 insertion in the promoter region, while strain SA137/93G is characterised by an insertion of IS256 into the gene tcaA. Although both insertions were shown to correlate with a decrease in susceptibility to vancomycin, the difference in the vancomycin resistance level of the strain pair could be mainly attributed to the disruption of tcaA in the mutant.This study was conducted to identify resistance mechanisms that both strains might have in common. To this end we compared the transcriptomes of both strains with that of the closely related vancomycin susceptible MRSA/VSSA strain SA1450/94 (MIC: 2 mg/L). We found that the genes of the capsule biosynthesis were the only genes with higher expression in both VISA strains.
Keywords: strain comparison

platform_organism: Staphylococcus aureus subsp. aureus N315

overall_design: For transcriptional profiling, the strains compared were grown in BHI to an optical density (600 nm) of 0.8-1.0. To guarantee statistical significance of the data, each experiment was replicated 4 times including a dye swap. RNA was isolated from two independent cultures of each strain. Each RNA preparation was used twice to synthesize cDNA resulting in four chips per competitive comparison.

first: Andrea

last: Jansen


title: Chloroplast-genome-wide maps of small RNAs in Chinese cabbage (Brassica rapa) and Arabidopsis thaliana (Ler).

status: Public on Mar 31 2012

city: Shanghai

first: Yu-ke

last: He

address: 300 Fenglin Road

institute: Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

type: Non-coding RNA profiling by high throughput sequencing

summary: Deep sequencing provided evidence that a novel subset of small RNAs were derived from the chloroplast genome of Chinese cabbage (Brassica rapa) and Arabidopsis (Ler). The chloroplast small RNAs (csRNAs) include those derived from mRNA, rRNA, tRNA and intergenic RNA. The rRNA-derived csRNA were preferentially located at the 3â-ends of the rRNAs, while the tRNA-derived csRNAs were mainly located at 5â-termini of the tRNAs. After heat treatment, the abundance of csRNAs decreased in chinese cabbage seedlings, except those of 24 nt in length. The novel heat-responsive csRNAs and their locations in the chloroplast were verified by Northern blotting. The regulation of some csRNAs to the putative target genes were identified by real-time PCR. Our results indicated that high temperature regulated the production of some csRNAs, which may have potential roles in transcriptional or post-transcriptional regulation, and affected putative target genes expression in chloroplast.

overall_design: Examination of two replicates of heat treated (HT) and control (MT) Chinese cabbage sample respectively, and one Arabidopsis (Ler) RNA sample.

first: Yu-Ke

first: Lu

last: Wang

first: Xiang

last: Yu

first: Han

first: Yi-Zhen

last: Lu

first: Marcel

last: Prins

first: Marjo

last: de Ruiter


title: Transcriptome analysis of 12 flowering ecotypes of Capsella bursa-pastoris

status: Public on Mar 13 2012

city: Guangzhou

first: Hui-Run

last: Huang

state: Guangdong

address: Xingke Road 723

institute: South China Botanical Garden, Chinese Academy of Sciences

summary: We used a digital gene expression (DGE) system to generate partial gene expression profiles for 12 selected samples. Significant differences in gene expression between early- and late-flowering samples were detected for 72 candidate genes for flowering time. Genes related to circadian rhythms were significantly overrepresented among the differentially expressed genes. Our data suggest that circadian clock genes play an important role in the evolution of flowering time, and C. bursa-pastoris plants exhibit expression differences for candidate genes likely to affect flowering time across the broad range of environments they face in China.

overall_design: Digital gene expression analysis was performed on RNA from 12 different flowering samples of C. bursa-pastoris. These samples are from different areas, 6 of which represent early-flowering ecotypes, and the other 6 samples represent late-flowering samples

first: Peng-Cheng

last: Yan

first: Martin

last: Lascoux

first: Xue-Jun

last: Ge


title: Genomic profiling of 19 renal cell carcinoma samples from patients with end-stage renal disease

status: Public on Apr 02 2012

city: Yufu-City, Oita

first: Toru

last: Inoue

address: Hasama-machi 1-1

department: Department of Molecular Pathology

institute: Faculty of medicineOita University

summary: In this study, 19 tumor samples from patients with renal cell carcinoma (RCC)-end-stage renal disease (ESRD) were analyzed by array comparative genomic hybridization (array CGH) using the Agilent Whole Human Genome 4× Array.

overall_design: 19 cystic disease samples from patients with RCC-ESRD

first: Keiko

last: Matsuura

first: Taichiro

last: Yoshimoto

first: Lam

middle: T

last: Nguyen

first: Yoshiyuki

last: Tsukamoto

first: Chisato

last: Nakada

first: Naoki

last: Hijiya

first: Takahiro

last: Narimatsu

first: Takeo

last: Nomura

first: Fuminori

last: Sato

first: Yoji

last: Nagashima

first: Kenji

last: Kashima

first: Shingo

last: Hatakeyama

first: Chikara

last: Ohyama

first: Tomonori

last: Habuchi

first: Masayuki

last: Nakagawa

first: Masao

last: Seto

first: Hiromitsu

last: Mimata

first: Masatsugu

last: Moriyama


title: Gene expression in a wild type strain (FGSC 2489) versus an Dime-2 strain (FGSC 17937) in Neurospora crassa during nitrogen starvation

status: Public on Feb 18 2012

city: Berkeley

first: Elizabeth

middle: Ann

last: Hutchison

state: CA

address: 111 Koshland Hall

department: Plant & Microbial Biology

country: USA

institute: UC Berkeley

summary: The protein kinase Ime2 is known to have an important role in meiosis in the yeast Saccharomyces cerevisiae. However, the Neurospora crassa IME2 homolog functions in self/nonself recognition as well as in the development of fungal sexual structures called protoperithecia. In N. crassa, protoperithecia are induced upon nitrogen starvation. We were interested in gene expression differences between an ime-2 deletion strain and a wild type strain, and due to the role of ime-2 during sexual development, carried out these arrays on media that was lacking in nitrogen.

overall_design: There is one condition and three samples in this experiment (wild type and Dime-2 strains grown on minimal media lacking nitrogen), and dye swaps were performed

first: N

middle: L

last: Glass


title: Profile of small RNA transcriptome during cortical development in the Rat

status: Public on Jun 26 2012

first: Maojin

last: Yao

address: 320# Yueyang Road

department: Neural circuit development

institute: Institute of Neurosciecne

summary: Small non-coding RNAs play important roles in regulating gene expression during development and disease. However, a comprehensive analysis of small RNAs in developing brain is largely lacking. By using next-generation sequencing technique, we carried out a systematic analysis of small RNA transcriptome of rat neocortex from early developmental stage till adult. Our results revealed an extraordinary degree of stage-specific profiling of miRNA, and other classes of small RNAs including snoRNA, rasRNA, scRNA and unexpectedly piRNA, which was considered to be solely expressed in germline tissues. Developmentally regulated miRNA editing was also observed. This study further showed the effectiveness of the high through-put sequencing in genome-wide analysis of small RNAs. The dataset described here will greatly contribute to our understanding of the divergence, variation, and function of small RNAs and may be a valuable resource in clarifying new regulatory mechanisms of cortical development.

overall_design: Identification and quantification of small RNA: forebrain and cortex from E10 to P28

first: Yuan

last: Xiaobing

first: Yao

last: Maojin

first: Chen

last: Gang


title: Pulmonary miRNA expression in C57BL/6 mice intratracheally instilled with Printex 90 carbon black nanoparticles

city: Ottawa

first: Andrew

last: Williams

state: ON

address: 50 Columbine

country: Canada

institute: Health Canada

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

overall_design: Refer to individual Series


title: Pulmonary miRNA expression in C57BL/6 non-pregnant female mice intratracheally instilled with Printex 90 carbon black nanoparticles

summary: miRNAs were measured in mice exposed to vehicle control (0.9% NaCl MilliQ water containing 10% v/v acellular BAL) or 0.162 mg Printex 90 in vehicle by intratracheal instillation and sacrificed 1, 3 and 28 days after exposure.

overall_design: C57BL/6 mice were exposed to 0.000 or 0.162 mg Printex 90 and sacrificed 1, 3 and 28 days after exposure. Individual total RNA enriched with small RNA from 6 mice per treatment group (control and 0.162mg) was hybridized to 8 x 15K Agilent miRNA slides.

first: Julie

middle: A

last: Bourdon

first: Anne

last: Saber

first: Sabina

last: Halappanavar

first: Petra

last: Jackson

first: Dongmei

last: Wu

first: Karin

last: Hougaard

first: Nicklas

middle: R

last: Jacobsen

first: Ulla

middle: B

last: Vogel

first: Håkan

last: Wallin

first: Carole

last: Yauk


title: Role of miRNAs in the neurogenesis of human neural stem cells

status: Public on Mar 01 2012

city: sacramento

first: jing

last: liu

address: 2921 Stockton Blvd

department: Stem Cell Program

institute: UC Davis

summary: by use of the model of human embryonic stem cell (hESC)-derived neurogenesis, miRNAs involved in the differentiation from neural stem cells (hNSC) to neurons were profiled and identified. HNSC were differentiated into the neural lineage, out of which the neuronal subset was enriched through cell sorting based on select combinatorial biomarkers: CD15-/CD29Low/CD24High. This relatively pure and viable subpopulation expressed the neuronal marker alpha III-tubulin. The miRNA array demonstrated that a number of miRNAs were simultaneously induced or suppressed in neurons, as compared to hNSC. Real-time PCR further validated the decrease in levels of miR214, but increase in brain-specific miR7 and miR9 in the derived neurons.

overall_design: This experiment includes a total of 6 samples which are divided in to 2 groups, each with 3 biological repeats: 3 untreated normal samples as controls and 3 differentiated samples as the treated condition

first: Jing

last: Liu

first: Jackline

last: Githinji

first: Bridget

last: Mclaughlin

first: Kasia

last: Wilczek

first: Jan

last: Nolta


title: Digital Gene Expression Analysis Based on Integrated De Novo Transcriptome Assembly of Sweet Potato [Ipomoea batatas (L.) Lam.]

city: Chengdu

first: Yinghong

last: Gu

address: No.24 South Section 1, Yihuan Road

institute: Sichuan University

summary: More than 3.5 million raw DGE tags were obtained in each library. The clean tags in each sample ranged from 3.35 to 3.63 million, and the distinct clean tags ranged from 93,593 to 139,389. The 21 bp DGE clean tags were mapped to sweet potato transcripts. Then, we compared 7 libraries pair-wisely so that 21 pairs of comparisons were implemented. Among these comparisons, we found that 4,721 to 12,151 transcripts had significant changes in expression, and the average number was 9,657. We also observed a large number of specifically expressed transcripts between each two libraries. The expression profiles of those genes involved in root development and carbohydrates accumulation were characterized. Moreover, other genes of interest, such as potentially abiotic stress tolerance and insect resistance, were also characterized.

overall_design: 7 samples are examined: young leaves, mature leaves, stems, fibrous roots, initial tuberous roots, expanding tuberous roots and harvest tuberous roots.

first: Yi

middle: Z

last: Zhang

first: Xiang

last: Tao

first: Ying

middle: H

first: Hai

middle: Y

last: Wang

first: Wen

last: Zheng

first: Xiao

last: Li

first: Chuan

middle: W

last: Zhao


title: Pulmonary miRNA expression in C57BL/6 Bom Tac mice (dams) intratracheally instilled with Printex 90 carbon black nanoparticles

first: Andrew

last: Williams

summary: miRNAs were measured in pregant mice exposed to vehicle control (nanopure water) or a cumulative dose of 0.268 mg Printex 90 in vehicle by intratracheal instillation and sacrificed at weaning (26-27 days after exposure).

overall_design: Pregnant mice were exposed to vehicle control (nanopure water) or a cumulative dose of 0.268 mg Printex 90 in vehicle by intratracheal instillation. Doses of 0.067 mg were delivered 4 times in pregnant females on gestational days 7, 10, 15 and 18. Mice were sacrificed at weaning (26-27 days post-exposure).

first: Sabina

last: Halappanavar

first: Petra

last: Jackson

first: Dongmei

last: Wu

first: Karin

last: Hougaard

first: Nicklas

last: Jacobsen

first: Ulla

first: Julie

last: Bourdon

first: Anne

last: Saber


title: Identification of long non-protein coding RNAs in chicken skeletal muscle by Solexa sequencing

status: Public on Feb 20 2012

first: Tingting

address: 38 Xueyuan Rd

department: Medical informatics

institute: Peking University

summary: Deep sequencing as a high-throughput technology has been widely used in the transcriptome profiling in mammals. In the present study, we aimed to identify chicken lncRNAs ranging from 300-1600 nt long. Total RNAs from chicken skeletal muscle at the embryonic stage were fractionated by 6% urea PAGE. Selected RNA fractions (300-1600 nt) were sequenced by Solexa technology.

overall_design:
Chicken eggs (White Leghorn) were incubated at 37.5°C for 10 days (E10), 12 days (E12), 14 days (E14), 18 days (E18). Skeletal muscles (pectoralis) were collected from chicken embryo incubated at above four stages. All muscle samples were immediately frozen in liquid nitrogen and stored at -80°C until RNA isolation. All embryonic manipulations were conducted in accordance with the protocols of the Chinese Academy of Medical Sciences and the Institutional Animal Care and Use Committee of Peking Union Medical College.

The single 'Chicken_muscle' Sample represents muscle pooled from all four stages.

first: Suya

first: Rimao

first: Yong

first: Dahai

last: Zhu


title: Toxicogenomics and phenotypic characterization of adult male zebrafish liver treated with benzo-[A]-pyrene (BAP)

status: Public on Jan 01 2012

city: Singapore

first: Choong Yong

last: UNG

address: 14 Science Drive 4

department: Department of Biological Sciences

country: Singapore

institute: National University of Singapore

summary: We performed microarray-based expression profiling on liver of male zebrafish exposed to 5, 50, and 500 µg/L of benzo-[A]-pyrene (BAP) for 24 and 96 hours, to identify global transcriptional programs and biological pathways involved in BAP-induced adaptive responses under in vivo environment.

overall_design: We analyzed 34 arrays of BAP-treated adult male zebrafish liver and 15 arrays of control fish.

first: Choong-Yong

last: Ung

first: Sie-Hong

last: Lam

first: Hlaing

middle: M

last: Myintzu

first: Sinnakarupan

last: Mathavan

first: Zhiyuan

last: Gong


title: Cell- and tissue-specific transcriptome analyses of Medicago truncatula root nodules

status: Public on May 29 2013

city: Hannover

first: Helge

last: Küster

address: Herrenhäuser Str. 2

department: Institut für Pflanzengenetik

institute: Leibniz Universität Hannover

summary:
We used laser-capture microdissection (LCM) to isolate specific cells from the Medicago truncatula nodule meristem (M), the distal infection (DIZ), the proximal infection zone (PIZ), infected cells (IC) and uninfected cells (UIC) from the fixation zone.
Based on Medicago GeneChips, we identified the cell- and tissue-specific programm of gene expression in  Medicago truncatula root nodules.

platform_organism:
Sinorhizobium meliloti
Medicago sativa
Medicago truncatula

overall_design: Nodules were harvested three weeks after inoculation of Medicago truncatula  (genotype Jemalong A17) plants with Sinorhizobium meliloti strain 2011. Nodules were fixed in Farmer's fixative and subsequently embedded in paraffin. 8 µm de-paraffined sections were used to capture cells from the nodule meristem, distal infection zone, proximal infection zone, infected cells and uninfected cells from the fixation zone, using an Arcturus Pixcell II laser capture microscope. 3 biological replicates were used for each cell-/tissue type. After RNA extraction, the RNA was amplified and used for Medicago Gene Chip hybridization.

first: Erik

last: Limpens

first: Sjef

last: Moling

first: Guido

last: Hooiveld

first: Patricia

last: Pereira

first: Ton

last: Bisseling

first: Jörg

middle: D

last: Becker


title: Expression data from porcine embryonic stem cells

status: Public on Dec 31 2011

city: Seoul

first: Jinkyu

last: Park

address: Gwanak-ro, Gwanak-gu

department: Agricultural Biotechnology

country: South Korea

institute: Seoul National University

summary: We have been able to derive EpiSC-like pESC lines from in vivo produced porcine blastocysts. Our cell lines showed AP activity, expressions of the genes Oct4, Sox2, Nanog, Rex1, TDGF1, bFGF, FGFR1, FGFR2, Nodal and Activin-A involved in pluripotency and signaling pathways and in vitro differentiation potential, displaying similarities to epiblast stem cells or hES cells.

overall_design: Porcine blastocysts were cultured on mitotically inactivated mouse embryonic fibroblasts (MEFs) in pESC medium. Following 5-7 days of culture, we observed EpiSC-like primary colonies derived from day 7 in vivo-produced. These EpiSC-like pESC colonies were mechanically dissociated into several clumps using pulled glass pipettes 10-15 days after seeding. Dissociated clumps were then re-seeded on fresh MEFs, and subsequent EpiSC-like pESC lines were routinely passaged via the pulled glass pipette method every 5-7 days. Our cell lines maintained stemness and a stable morphology for more than 56 passages. The main purpose of the present study was to investigate gloval gene expression from porcine embryonic stem cells.

first: Hye-Young

last: Son

first: Jin-kyu

first: Hye-Sun

last: Kim

first: Chang-Kyu

last: Lee


title: SuperSAGE data from skunk cabbage spadices

status: Public on Dec 22 2011

city: Miyazaki

first: Takehito

last: Inaba

state: Miyazaki

address: 1-1 Gakuenkibanadai-nishi

department: Interdisciplinary Research Organization

institute: University of Miyazaki

summary: This study aims at investigating the gene expression profile of thermogenic skunk cabbage (Symplocarpus renifolius). Using Super-SAGE, we compared the gene expression profile of different developmental stages of skunk cabbage spadices.

overall_design: To obtain the SuperSAGE libraries, we followed the original SuperSAGE protocol described by Matsumura and colleagues (Matsumura et al., 2003) with some modification. Total RNA of spadices in different developmental stage (immature, female, bisexual, and male) were isolated using RNAiso reagent. The SuperSAGE library was directly sequenced with a large-scale pyrosequencing method.

first: Yasuko

last: Ito-Inaba

first: Hideo

last: Matsumura

first: Ryohei

last: Terauchi


title: Small RNA profiling in two Brassica napus cultivars identifies microRNAs with oil production and developmental correlated expressions and new small RNA classes

status: Public on Dec 28 2011

city: Old Westbury

first: Ying-Tao

last: Zhao

state: NY

address: Riland building, Room 024 Northern Boulevard, P.O. Box 8000

department: Biomedical Sciences

institute: New York Institute of Technology

summary: MicroRNAs and siRNAs are important regulators of plant development and seed formation, yet their population and abundance in the oil crop Brassica napus are still less understood, especially at different developmental stages and among cultivars with varied seed oil contents. Here, we systematically analyzed the small RNA expression profiles of Brassica napus seeds at early embryonic developmental stages in a high oil content and a low oil content Brassica napus cultivars, both cultured in two environments. A total of 50 conserved miRNAs and 11 new miRNAs were identified, together with some new miRNA targets. Expression analysis revealed some miRNAs with varied expression levels in different seed oil content cultivars or at different embryonic developmental stages. A large amount of 23-nt small RNAs with specific nucleotide composition preference were also identified, which may present new classes of functional small RNAs.

overall_design: Examination of small RNA profiles in 2 different seed oil content rapeseed culvitars at 2 locations.

first: Meng

last: Wang

first: Xiu-Jie


title: Development of gene expression signatures for practical radiation biodosimetry

status: Public on Apr 09 2012

first: Fu

last: Shijun

address: Halei Road

institute: China Novartis Institutes for BioMedical Research

summary: Genome-wide analysis of miRNA expression was performed in Activin A and Wnt3a-treated mouse ESCs during the different stages of DE differentiation to identify candidate miRNAs likely to be involved in Wnt3a and Activin A induced DE formation. Our analysis exhibited a distinct miRNA expression finger print. Furthermore, we found that forced expression of a subset of synergistically regulated miRNAs could partially mimic the roles of Wnt3a and Activin A. Pathway analyses also revealed the involvement of histone acetylation in Activin A/Wnt3a-driven DE differentiation, which is further confirmed by treating the cells with small molecular weight HDAC inhibitors as well as ChIP experiments. Our study established a regulatory cascade from extracellular cytokine treatment to miRNA expression to histone modification in cell nucleus during DE differentiation.

overall_design: ESCs were treated with 100ng/ml Activin A, or 50ng/ml Wnt3a, or 100ng/ml Activin A plus 50ng/ml Wnt3a, and the samples were collected at 1 day, 3 days, and 5 days after treatment, respectively. Cells treated with the same medium without growth factors were used as the negative controls for each time point.

first: Shijun

last: Fu

first: Qi

last: Fei

first: Hua

last: Jiang

first: Shannon

last: Chuai

first: Wen

last: Xiong

first: Lei

first: Chris

last: Lu

first: Peter

last: Atadja

first: En

last: Li

first: Jianyong

last: Shou


title: Sequencing-based approaches reveal low ambient temperature-responsive and tissue-specific microRNAs in Phalaenopsis orchid

status: Public on Dec 12 2011

city: Tainan

first: Feng-Ming

last: An

address: No. 59, Silaya Blvd., Sinshi Dist.

department: Biotechnology Center in Southern Taiwan

country: Taiwan

institute: Academia Sinica

summary: We performed four small RNA sequencing for identification and characterization of microRNAs in Phalaenopsis aphrodite subsp. formosana. By comparing the low temperature-treated group with treated group, we concluded four miRNAs - miR156, miR162, miR528 and miR535 -  as low temperature-induced miRNAs. In addition, tissue-specific expression of these miRNAs was investigated. The files contain the miRNAs analysis results in each group.

overall_design: Examination of low temperature-treated leaves and two other organs of Phalaenopsis orchid

first: Shuan-Rung

last: Hsiao

first: Ming-Tsair

last: Chan


title: Aedes aegypti embryos

status: Public on Dec 16 2011

city: Blacksburg

first: Zhijian

last: Tu

state: VA

address: 309 Engel Hall

department: Biochemistry

institute: Virginia Tech

summary: RNA-Seq was used for transcriptome sequencing of 0-12 hour embryos.

overall_design: RNA was isolated from described samples for RNA-Seq. Samples fromfour embryonic time points from 0-12 hr. Raw data not provided.


title: Programmed fluctuations in sense/anti-sense transcript ratios drive sexual differentiation in Schizosaccharomyces pombe

status: Public on Dec 20 2011

city: London

first: Danny

middle: Asher

last: Bitton

address: Darwin Building, Gower Street

department: Department of Genetics, Evolution & Environment

country: United Kingdom

institute: University College London

summary: Strand specific RNA sequencing of S. pombe revealed a highly structured programme of ncRNA expression at over 600 loci. Waves of antisense transcription accompanied sexual differentiation. A substantial proportion of ncRNA arose from mechanisms previously considered to be largely artefactual, including improper 3’ termination and bi-directional transcription. Constitutive induction of the entire spk1+, spo4+, dis1+ and spo6+ antisense transcripts from an integrated, ectopic, locus disrupted their respective meiotic functions. This ability of antisense transcripts to disrupt gene function when expressed in trans suggests that cis production at native loci during sexual differentiation may also control gene function. Consistently, insertion of a marker gene adjacent to the dis1+ antisense start site mimicked ectopic antisense expression in reducing the levels of this microtubule regulator and abolishing the microtubule-dependent “horsetail” stage of meiosis. Antisense production had no impact at any of these loci when the RNAi machinery was removed. Thus, far from being simply ‘genome chatter’, this extensive ncRNA landscape constitutes a fundamental component in the controls that drive the complex programme of sexual differentiation in S. pombe.

overall_design: Thorough interrogation of the Schizosaccharomyces pombe transcriptome during sexual differentiation using strand-specific total RNA sequencing (AB SOLiD 3.0 and 3.0+). A total of 19 samples were analysed by two separate machine runs (henceforth first and second runs, respectively). In the first machine run the following 5 samples were processed (on a single sequencing slide): Vegetative haploid (strain IH5974), pat1.114 diploid (IH2912) at vegetative growth (0) and pat1.114 diploid (IH2912) at 3, 5 and 10 hours following temperature shift from 25ºC to 32ºC to induce meiosis by Pat1 inactivation. In the second machine run the following 14 samples were processed (on two sequencing slides): Vegetative haploid (IH5974), pat1.114 diploid (IH2912) at vegetative growth (0) and pat1.114 diploid (IH2912) at 3, 5 and 10 hours following the temperature shift (a biological replicate of the first machine run). In addition, asynchronous IH3365 (wild type diploid) was also sequenced to enable a series of pair-wise haploid/diploid comparisons between itself, asynchronous haploid (IH5974) and pat1.114 diploid (IH2912) at vegetative growth. Finally, to find putative targets of the two bzip transcription factors atf21 and atf31, we sequenced RNA extracts from IH8832 (atf21.delta diploid) and IH8814 (atf31.delta diploid) before (0), and 3, 5, and 10 hours after the temperature shift, while the pat1.114 diploid (IH2912) at vegetative growth (0) and pat1.114 diploid (IH2912) at 3, 5 and 10 hours following the temperature shift were used as reference for this analysis.

first: Agnes

last: Grallert

first: Paul

middle: J

last: Scutt

first: Tim

last: Yates

first: James

last: Bradford

first: Yaoyong

first: Yvonne

last: Hey

first: Stuart

last: Pepper

first: Iain

last: Hagan

first: Crispin

last: Miller


title: Massive analysis of rice small RNAs: Mechanistic implications of regulated miRNAs and variants for differential target RNA cleavage

city: NEWARK

first: Dong-Hoon

last: Jeong

state: DE

address: 15 Innovation Way

institute: University of Delaware

summary: Small RNAs have variety of important roles in plant development, stress responses, and other processes. They exert their influence by guiding mRNA cleavage, translational repression, and chromatin modification. To identify novel and regulated rice miRNAs, 62 small RNA libraries were constructed from rice plants and deeply sequenced with Illumina technology. The libraries represent several tissues from control plants and plants subjected to different environmental stress treatments. More than 94 million genome-matched reads were obtained resulting in more than 16 million distinct small RNA sequences. This allowed an evaluation with current criteria of about 400 annotated miRNAs and the finding that among these, about 150 had siRNA-like characteristics. Seventy nine new miRNAs were identified and miRNAs were distinguished that are regulated in response to water stress, nutrient stress, or temperature stress. Among the new examples of miRNA regulation were members of the same miRNA family that were differentially regulated in different organs and had distinct sequences Some of these distinct family members result in differential target cleavage and provide new insight about how an agriculturally important rice phenotype could be controlled in the panicle. This high resolution analysis of rice miRNAs should be relevant to plant miRNAs in general, particularly in the Poaceae.

overall_design: Examination of different tissue types and  tissues treated with various environmental and nutrient stresses in rice by high throughput sequencing for small RNA profiling

first: Pamela

last: Green


title: Comparability and concordance of replicated microarray data.

status: Public on Sep 29 2011

city: Toronto

first: Dong-Yu

last: Wang

address: 610 University Ave

institute: UHN-PMH-OCI

summary: To measures the comparability and concordance of Illumina microarray, a series of 30 samples of Universal Human Reference RNA (UHRR) were set as controls for every single chip of total 30 Human-Ref V2 BeadChips. The average bead number of the 30 arrays was 42.3±8.1 for any bead type over the 22,184 probes. A high average correlation coefficient (r) value was obtained as 0.9908±0077 relative to each other of the expression intensity values from the 30 duplicate UHRR samples.

overall_design: 30 UHRR (Stratagene; La Jolla, CA) samples were used as controls for each of 30 BeadChips.

first: Dong

first: Wey

last: Leong


title: Transcriptional profiling of the Neurospora crassa Δcre-1 mutant (FGSC 10372) compared to the wild type strain (FGSC 2489) in response to minimal medium or Avicel medium

status: Public on Jul 21 2011

first: Jianping

last: Sun

address: 111 Koshland Hall

institute: UC Berkeley

summary: In filamentous ascomycete fungi, the utilization of alternate carbon sources is influenced by the zinc finger transcription factor CreA/CRE-1, which encodes a carbon catabolite repressor protein homologous to Mig1 from Saccharomyces cerevisiae. In Neurospora crassa, deletion of cre-1 results in increased secretion of amylase and β-galactosidase. Here, we determined the CRE-1 regulon by investigating the transcriptome of a Δcre-1 strain compared to wild type when grown on Avicel versus minimal medium (MM). Our data provide comprehensive information on the CRE-1 regulon in N. crassa and contribute to deciphering the global role of carbon catabolite repression in filamentous ascomycete fungi during plant cell wall deconstruction.

overall_design: Two-condition experiment (minimal medium vs. Avicel medium) of the Δcre-1 mutant strain compared to the wild type strain. Cy3 and Cy5 dye swaps were performed.

first: N

last: Glass


title: The Polycomb group mutant esc leads to augmented the levels of paused Pol II in the Drosophila embryo.

status: Public on Jun 15 2011

city: Corvallis

first: David

middle: Anthony

last: Hendrix

state: OR

address: 2011 Ag & Life Sciences Bldg

department: Biochemistry and Biophysics/EECS

institute: Oregon State University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The role of Polycomb group (PcG) was studied on RNA Polymerase II (Pol II) pausing phenomenon. Wild type and Polycomb mutant (esc) embryos were used for ChIP-Seq experiments using Pol II and histone methylation antibodies. Enhanced Pol II occupancy was observed for thousands of genes in esc mutant embryos, including genes not known to be bound by PRC2 or having H3K27me3 associated. Most of these genes exhibit a concomitant reduction in H3K27me3 and increase in H3K4me3 at promoter-proximal regions. Silent genes lacking promoter-associated paused Pol II in wild-type embryos are converted into âpoisedâ genes with paused Pol II in esc mutants. We suggest that this conversion of silent genes into poised genes might render differentiated cell types susceptible to switches in identity in PcG mutants.

overall_design: ChIP-Seq data was generated for antibodies against Pol-II, H3K4me3, H3K27me3 in both wild type and esc mutant Drosophila embryos (0-2hr, 8-12hr, and 18-24hr embryos). In addition GRO-Seq data was generated for 18-24hr esc mutant embryos.

first: Vivek

middle: S

last: Chopra

first: Leighton

last: Core

first: Chiahao

last: Tsui

first: John

last: Lis

first: Michael

last: Levine


title: High-throughput sequencing of small RNAs in Triticum aestivum

status: Public on Sep 30 2011

city: Udine

first: Emanuele

last: De Paoli

state: UDINE

address: via delle Scienze 206

department: Agricultural, Food, Environmental and Animal Sciences

country: Italy

institute: University of Udine

summary: Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Triticum aestivum tissues (including leaves and spiklets infected with Fusarium and control). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the genome under study.

overall_design: Small RNA libraries were derived from leaves and spiklets control and Fusarium-infected of Triticum aestivum. Total RNA from leaves was isolated usingTriReagent (Molecular Research Center)and from spikelets using the Plant RNA Purification Reagent (Invitrogen), and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Yang Yen for providing the plant material as well as Kan Nobuta and Gayathri Mahalingam for assistance with the computational methods.

first: Monica

last: Accerbi

first: Blake

middle: C

last: Meyers


title: Androgen receptor cistrome in breast cancer cell line MDA-MB-453 with 5a-dihydrotestosterone (DHT) stimulation

status: Public on Jul 11 2011

city: Houston

first: Yiwen

last: Chen

state: TX

address: 1400 Pressler Street

department: Bioinformatics and Computational Biology

institute: University of Texas MD Anderson Cancer Center

summary: Androgen receptor (AR) is expressed in 60-70% of breast cancers independent of estrogen receptor (ER) expression, however its function in breast cancer is largely unknown. Our study identified the high level of AR in ERâ/HER2+ breast tumors and andorgen and AR greatly stimulated growth of MDA-MB-453 breast cancer cells. To define the genome-wide AR binding sites, we performed AR ChIP-seq using MDA-MB-453 breast cancer cells followig stimulation of DHT. We also identified FOXA1 is a crucial AR cofactor in MDA-MB-453 cells and the FOXA cistrome showed signaficant overlap with AR at both early and late time points of DHT stimulation.

overall_design: AR ChIP was performed in MDA-MB-453 breast cancer cells following 5a-dihydrotestosterone (DHT) stimulation for 4h and 16h respectively. FOXA1 ChIP-seq was performed after 4h DHT stimulation in MDA-MB-453 cells.

first: Min

last: Ni

first: Myles

last: Brown


title: Tannic acid (20 µg/ mL) treatment effect on transcriptome of Pseudomonas fluorescens Pf-5

status: Public on Nov 24 2011

city: Hong Kong

first: Chee Kent

last: Lim

address: Kowloon Tong

department: School of Energy and Environment

country: Hong Kong

institute: City University of Hong Kong

summary: Transcriptomic profiling of Pseudomonas fluorescens Pf-5 comparing culture treated with 20 µg/mL tannic acid against non-treated culture grown in Mueller-Hinton media

overall_design: Two-condition experiment, tannic acid (20 µg/ mL) treated culture versus non-treatment culture. 3 biological replicates including 3 technical replicates for one of the biological replicate and 2 technical replicates for another biological replicate. Swap-dye experiments were performed

first: Chee-Kent

first: Karl

last: Hassan

first: Anahit

last: Penesyan

first: Joyce

middle: E

last: Loper

first: Ian

middle: T

last: Paulsen


title: High-throughput sequencing of small RNAs in Vitis vinifera

summary: Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Vitis vinifera tissues (including leaves, flowers and berries). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the genome under study.

overall_design: Small RNA libraries were derived from leaves flowers and berries of Vitis vinifera. Total RNA was isolated using the Plant RNA Purification Reagent (Invitrogen), and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Gabriele Di Gaspero for providing the plant material as well as Kan Nobuta and Gayathri Mahalingam for assistance with the computational methods.

first: Pamela

last: Green


title: Molecular characterization of Nodal marginal zone lymphoma [CGH]

city: Toledo

first: Alberto

last: Arribas

state: Toledo

address: Avda Barber, 30

department: Molecular Pathology Research Unit

country: Spain

institute: Hospital Virgen de la Salud

summary: Nodal marginal zone lymphoma (NMZL) is a small B cell neoplasm whose molecular pathogenesis is still essentially unknown and whose differentiation from other small B cell lymphomas is hampered by the lack of specific markers. We have analyzed gene expression, miRNA profile and copy number data from 15 NMZL cases. For comparison, 16 follicular lymphomas, 9 extranodal marginal zone lymphomas, 8 reactive lymph nodes and B-cell subtypes were included. The results were validated by qRT-PCR in an independent series including 61 paraffin-embedded NMZLs. NMZL signature showed an enriched expression of gene sets identifying interleukins, integrins, CD40, PI3K, NF-kB and TGF-Beta; and included genes expressed by normal marginal zone cells and memory B cells. The most highly overexpressed genes were SYK, TACI, CD74, CD82 and CDC42EP5. Genes linked to G2/M and germinal center were downregulated. Comparison of the gene expression profiles of NMZL and FL showed enriched expression of CHIT1, TGFB1 and TACI in NMZL, and BCL6, LMO2 and CD10 in FL. NMZL displayed increased expression of miR-221, miR-223 and let-7f, while FL strongly expressed miR-494. Our study identifies new candidate diagnostic molecules for NMZL and reveals survival pathways activated in NMZL.

overall_design: Copy number alteration (CNA) was assayed with the DNA from 14 NMZL of frozen-tissue cases, extracted using the standard phenol-chloroform protocol. For CNA, the DNA was hybridized on an Agilent Human Genome CGH Microarray Kit 1 x 44K (Agilent Technologies) following the manufacturer’s instructions. Human female and male pooled gDNA (Promega) was used to normalize the CGH results. Results were considered valuable in 12 cases. The samples (1 μg DNA) were labeled with Cy5 and the DNA donor pool was labeled with Cy3.

first: J

first: Y

last: Campos-Martín

first: C

last: Gómez-Abad

first: P

last: Algara

first: M

last: Sánchez-Beato

last: Rodriguez-Pinilla

first: S

last: Montes-Moreno

first: N

last: Martinez

last: Alves-Ferreira

last: Piris

last: Mollejo


title: Human rectal adenoma (8 cases) vs. rectal carcinoma (8 cases)

city: Beijing

first: Ming-Rong

last: Wang

address: 17 Panjiayuan Nanli, Chaoyang District, Beijing, China

institute: Cancer Institute (Hospital), Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China

summary: Genomic profiling of human rectal adenoma and carcinoma by array-based comparative genomic hybridization

overall_design: Two group experiment, rectal adenoma vs. rectal carcinoma. Biological replicates: 8 adenomas vs. 8 carcinomas

first: Zhi-Zhou

last: Shi


title: Tannic acid (160 µg/ mL) treatment effect on transcriptome of Pseudomonas fluorescens Pf-5

first: Chee Kent

last: Lim

summary: Transcriptomic profiling of Pseudomonas fluorescens Pf-5 comparing culture treated with 160 µg/mL tannic acid against non-treated culture grown in Mueller-Hinton media

overall_design: Two-condition experiment, tannic acid (160 µg/ mL) treated culture versus non-treatment culture. 3 biological replicates including 3 technical replicates for one of the biological replicate and 2 technical replicates for another biological replicate. Swap-dye experiments were performed

last: Hassan

last: Penesyan


title: High-throughput sequencing of small RNAs in Solanum lycopersicum

first: Emanuele

last: De Paoli

summary: Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Solanum licopersicum tissues (including leaves, flowers and fruit). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the genome under study.

overall_design: Small RNA libraries were derived from  leaves, flowers and fruit of Solanum lycopersicum. Total RNA was isolated using the Plant RNA Purification Reagent (Invitrogen), and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Harry Klee for providing the plant material as well as Kan Nobuta and Gayathri Mahalingam for assistance with the computational methods.

first: Monica

last: Accerbi

last: Green

first: Blake

last: Meyers


title: Tannic acid treatment effect on transcriptome of Pseudomonas fluorescens Pf-5

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

overall_design: Refer to individual Series


title: CpG context and content in evolutionary signatures of brain DNA methylation

status: Public on Oct 05 2011

city: New York

first: Fatemeh

last: Haghighi

address: 1051 Riverside Drive, Box 42

institute: Columbia University

type: Methylation profiling by high throughput sequencing

summary: We assayed CpG methylation in cerebral cortex of neurologically and psychiatrically normal human postmortem specimens, as well as mouse forebrain specimens. Cross-species human-mouse DNA methylation conservation analysis shows that DNA methylation is not correlated with sequence conservation. Instead, greater DNA methylation conservation is correlated with increasing CpG density. We identified key genomic features that can be targeted for identification of epigenetic loci that may be developmentally and evolutionarily conserved and wherein aberrations in DNA methylation patterns can confer risk for disease.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Characterization of evolutionary signatures of DNA methylation in the brain

first: Yurong

last: Xin


title: Neurospora crassa wild-type cells (WT, FGSC 2489) undergoing a time-course treatment with staurosporine

city: Porto

first: Arnaldo

last: Videira

address: Rua Campo Alegre 823

country: Portugal

institute: IBMC-Instituto de Biologia Molecular e Celular

summary: Staurosporine induces programmed cell death in a series of organisms. Here, we analyse gene expression of the filamentous fungus Neurospora crassa following exposure to staurosporine for different time periods.

overall_design: Cells incubated for 15, 30, 60 and 120 min in the presence (S) or absence (C) of staurosporine were compared; Cy3 and Cy5 dye swap

middle: L

last: Glass


title: Transcriptome profiling analysis of bacterial challenged Lateolabrax japonicus reveals deep insight into the immune-relevant genes in marine fish (DGE)

status: Public on Jun 13 2011

city: HangZhou

first: Ding

last: He

state: ZheJiang

address: YuHangTang road

department: College of Life Science

institute: ZheJiang University

summary: We report the application of Solexa/Illumina's digital gene expression (DGE) sequencing approaches to investigate inactivated Vibrio harveyi--induced transcriptome changes in Lateolabrax japonicas, a non model vertebrate species. Totally 3.44 and 3.22 million raw tags were measured. Then, gene annotation was performed by tags mapping analysis and the 169,950 non-redundant consensus sequences from RNA-seq based transcriptome analysis were used as reference transcript database. Tag mapping indicated that Vibrio harveyi--challenged adult Lateolabrax japonicas express over 70% of all genes represented in transcript databases. Meanwhile, totally 1224 consensus sequences exhibited significant difference after the bacterial challenge, in which 1183 transcripts can be well annotated, while approximately 41 transcripts have low sequence homology to the existing known sequences in public databases, suggesting that they might be putative novel immune-relevant genes in Lateolabrax japonicus closely related to the immunity for bacterial challenge. Our present study would greatly benefit to give deep insight into the immunogenetics in fish species, and clinical application in fish diseases.

overall_design: Examination of differentially expressed transcripts in baterial- and mock challenged fish.

first: Jian-zhong

last: Shao

first: Li-xin

last: Xiang

first: Wei-ren

last: Dong

first: Yiwen

last: Zhang


title: High-throughput sequencing of small RNAs in Silene latifolia

summary: Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Silene latifolia tissues (including leaves, flowers and smutted flowers). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the genome under study.

overall_design: Small RNA libraries were derived from female leaves, female flowers and female flowers smutted of Silene latifolia. Total RNA was isolated using the TriReagent (Molecular Research Center), and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Manfred Ruddat for providing the plant material as well as Kan Nobuta and Gayathri Mahalingam for assistance with the computational methods.

first: Pamela


title: Mapping the DNA-binding response regulators of Desulfovibrio vulgaris Hildenborough

status: Public on May 31 2011

city: Berkeley

first: Lara

last: Rajeev

address: 1 Cyclotron Road

institute: Lawrence Berkeley Lab

type: Genome binding/occupancy profiling by genome tiling array

summary:
D. vulgaris is a model sulfate reducing bacteria whose genome encodes a high number of two component systems, including 29 DNA-binding response regulators (RRs) whose functions are unknown, but are very likley to be important to the environmental lifestyle of the organism. We determined the gene targets for 24 of these RRs using purified His-tagged RR and sheared genomic DNA in an in vitro DAP-chip (DNA-affinity-purified - chip) assay. For each RR, one target was identified first using gel shift assays, and qPCR was used to ensure that the target was enriched in the RR-bound DNA before the samples were hybridized to a tiling array.
Based on the peaks generated by the array analysis, we determined that at least 200 genes are regulated by two component systems in this organism. We also predicted binding site motifs and validated them for 15 RRs using gel shift assays.

platform_organism: Nitratidesulfovibrio vulgaris str. Hildenborough

overall_design: In vitro DAP-chip for 28 response regulators where RR-bound enriched DNA is compared to input total genomic DNA

first: Eric

last: Luning

first: Adam

last: Arkin

first: Aindrila

last: Mukhopadhyay


title: High-throughput sequencing of small RNAs in Setaria italica

last: De Paoli

summary: Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Setaria italica tissues (including leaves, flowers and roots). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the genome under study.

overall_design: Small RNA libraries were derived from seedling leaves, flowers and roots harvested 5-6 weeks after initial planting of Setaria italica. Total RNA was isolated using the Plant RNA Purification Reagent (Invitrogen), and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Jeff Bennetzen for providing the plant material as well as Kan Nobuta and Gayathri Mahalingam for assistance with the computational methods.


title: High-throughput sequencing of small RNAs in Populus trichocarpa

status: Public on May 10 2011

summary: Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Populus trichocarpa tissues (including leaves, xylem and mechanically-treated xylem). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the maize genome under study.

overall_design: Small RNA libraries were derived from  leaves, xylem and mechanically-treated xylem of Populus trichocarpa, Nisqually-1 genotype. Total RNA was isolated using the Plant RNA Purification Reagent (Invitrogen), and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Vincent Chiang  for providing the plant material as well as Kan Nobuta and Gayathri Mahalingam for assistance with the computational methods.

last: Accerbi


title: mRNA-seq data of embryonic chicken digits

status: Public on Sep 08 2011

city: West Haven

first: Zhe

last: Wang

state: CT

address: 300 Heffernan Drive, B31-RA269

institute: Yale University

summary: Morphological characters are the result of developmental gene expression. Hence the identity of a character is ultimately grounded in the gene regulatory network directing development and thus whole genome gene expression data can provide evidence about character identity. Here we use transcriptomic data to address one of the most enduring paradoxes in evolutionary biology, the identity of the avian wing digits. Deep Sequencing of mRNA from embryonic chicken digits is performed and the gene expression profiles are analyzed.

overall_design: Analysis of mRNA-seq data from 16 samples of chicken digits covering two embryonic stages.

first: Rebecca

last: Young

first: GÃ¼nter

middle: P

last: Wagner


title: High-throughput sequencing of small RNAs in Solanum tuberosum

first: Emanuele

summary: Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Solanum tuberosum tissues (including leaves, flowers and stolon). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the genome under study.

overall_design: Small RNA libraries were derived from  leaves, flowers and stolon of Solanum tuberosum. Total RNA was isolated using the Plant RNA Purification Reagent (Invitrogen), and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Barbara Baker  for providing the plant material as well as Kan Nobuta and Gayathri Mahalingam for assistance with the computational methods.

first: Monica

last: Green

first: Blake

last: Meyers


title: High-throughput sequencing of small RNAs in Picea abies

summary: Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Picea abies tissues (including needles, immature cones and lateral bud meristem). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the maize genome under study.

overall_design: Small RNA libraries were derived from  needles, immature female cones and lateral bud meristem of Picea abies. Total RNA was isolated using the Plant RNA Purification Reagent (Invitrogen), and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank David Neale  for providing the plant material as well as Kan Nobuta and Gayathri Mahalingam for assistance with the computational methods.


title: Transcriptomic assessment of resistance to effects of an aryl hydrocarbon receptor (AHR) agonist in embryos of Atlantic killifish (Fundulus heteroclitus) from a marine Superfund site

status: Public on Jun 06 2011

city: Miami

first: Marjorie

middle: F.

last: Oleksiak

state: FL

address: 4600 Rickenbacker Causeway

department: Marine Biology and Fisheries

institute: University of Miami

summary: This study presents statistical analyses of gene expression in 5, 10 and 15 day post-fertilization (dpf) embryos of the teleost Fundulus heteroclitus treated with control vehicle (DMSO) or a potent non-ortho-PCB (PCB-126; 3,3’,4,4’,5-pentachlorobiphenyl).  The embryos were from two populations: a clean, reference population (SC, Scorton Creek, MA USA) and a polluted Superfund population (N, New Bedford Harbor, MA USA).  For each site, eggs from 8 females (~1100 total) were fertilized using minced testes from 5 males. After non-fertile eggs were culled, embryos were exposed to vehicle (DMSO; 0.1%) or PCB-126 (50 nM) in filtered seawater (salinity 25 part per thousand, 65 embros per 20 ml in glass petri dish) for 4 hr at 20º C. After exposure, the embryos were washed in filtered seawater and incubated at 20º C under a 14-h light, 10-h dark cycle.  At 5-, 10-, and 15-dpf, embryos were collected as three pools of 20 embryos from each treatment group and flash frozen in liquid nitrogen and stored at -80º C until used for RNA isolation.

overall_design: A loop design was used for the microarray hybridizations where each sample is hybridized to 2 arrays using both Cy3 and Cy5 labeled fluorophores. We used three loops in which each loop consisted of Cy3- and Cy5-labeled embryo aRNAs from 12 samples: one sample from each population-treatment-time combination.  Within a population-treatment-time, embryos were randomly assigned to one of the three loops.  In total, 36 embryos were hybridized to 36 microarrays.  The loops formed were SC5C→ SC5P → NBH5C→ NBH5P →SC10C→ SC10P→ NBH10C→ NBH10P → SC15C→ SC15P → NBH15C → NBH15P → SC5C, where each arrow represents a separate hybridization (array) with the biological sample at the base of the arrow labeled with Cy3 and the biological sample at the head of the arrow labeled with Cy5.  SC represents the Scorton Creek, Sandwich, MA population (reference), NBH represents the New Bedford Harbor, MA population, C represents control dose (DMSO), P represents the PCB-126 dose, 5 represents 5 dpf, 10 represents 10 dpf and 15 represents 15 dpf.

middle: F

first: Sibel

middle: I

last: Karchner

first: Mathew

last: Jenny

first: Diana

middle: G

last: Franks

first: David

last: Mark Welch

first: Mark

last: Hahn


title: High-throughput sequencing of small RNAs in Sorghum bicolor

summary: Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Sorghum bicolor tissues (including leaves, flowers and panicle). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the genome under study.

overall_design: Small RNA libraries were derived from  leaves, flowers and panicle of Sorghum bicolor. Total RNA was isolated using the Plant RNA Purification Reagent (Invitrogen), and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Patricia Klein for providing the plant material as well as Kan Nobuta and Gayathri Mahalingam for assistance with the computational methods.

first: Pamela


title: Interspecies Pinaceae comparison experiment

status: Public on Feb 16 2012

city: Québec

first: John

last: MacKay

state: Québec

address: 1030, avenue de la Médecine, Pavillon C.-E. Marchand

department: Centre d'étude de la forêt

institute: Université Laval

summary: The goal of this experiment is to evaluate the potential for utilising this oligonucleotide microarray in other species and genera of the Pinaceae family by using comparative RNA hybridizations in four different spruces (Picea spp), two pines (Pinus spp.) and a larch (Larix laricina), across two tissues, xylem and phelloderm.

sample_organism:
Larix laricina
Picea abies
Picea glauca
Picea sitchensis
Picea mariana
Pinus strobus
Pinus resinosa

platform_organism:
Picea glauca
Picea sitchensis

overall_design: One-color comparison of 7 conifer species in 2 tissue types: xylem and phelloderm. Between 4 and 28 biological repetitions per sample type, depending on the species, for a total of 142 slides.

first: Elie

last: Raherison

first: Sébastien

last: Caron

first: Isabelle

last: Giguère


title: High-throughput sequencing of small RNAs in Nuphar advena

last: De Paoli

summary: Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Nuphar advena tissues (including leaves, flowers and roots). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the maize genome under study.

overall_design: Small RNA libraries were derived from  leaves, flowers and fruit of Nuphar advena. Total RNA was isolated using the Plant RNA Purification Reagent (Invitrogen) for leaves and the Guanidinium-free for flowers and roots, and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Claude dePamphilis  for providing the plant material as well as Kan Nobuta and Gayathri Mahalingam for assistance with the computational methods.


title: High-throughput sequencing of small RNAs in Marsilea quadrifolia

summary: Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from different Marsilea quadrifolia tissues  (leaves, roots and drought-treated leaves). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the maize genome under study.

overall_design: Small RNA libraries were derived from leaves, roots and drought-treated leaves . Total RNA was isolated using the Plant RNA Purification Reagent  (Invitrogen) (roots) and the TriReagent (Molecular Research Center) (leaves) and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Dina Mandoli for providing the plant material and Kan Nobuta and Gayathri Mahalingam for assistance with the computational methods..

last: Accerbi


title: High-throughput sequencing of small RNAs in Mimulus guttatus

summary: Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Mimulus guttatus tissues (including leaves, flowers and roots). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the maize genome under study.

overall_design: Small RNA libraries were derived from  leaves, flowers and roots of Mimulus guttatus, strain âIM62â. Total RNA was isolated using the Plant RNA Purification Reagent (Invitrogen), and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank John Willis  for providing the plant material as well as Kan Nobuta and Gayathri Mahalingam for assistance with the computational methods.


title: High-throughput sequencing of small RNAs in Musa acuminata

summary: Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Musa acuminata tissues (including leaves, male flowers and immature fruit). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the maize genome under study.

overall_design: Small RNA libraries were derived from  leaves, male flowers and immature fruit of Musa acuminata. Total RNA was isolated using the Plant RNA Purification Reagent (Invitrogen), and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank  Nicolas Roux for providing the plant material as well as Kan Nobuta and Gayathri Mahalingam for assistance with the computational methods.


title: High-throughput sequencing of small RNAs in Gossypium arboreum

summary: Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from different Gossypium arboreum tissues  (leaves, flowers and fibers). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the maize genome under study.

overall_design: Small RNA libraries were derived from leaves, flowers and fibers of Gossypium arboreum. Each tissue represented a mixture of developmental stages. Total RNA was isolated using the Plant RNA Purification Reagent (Invitrogen) and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Thea Wilkins for providing the plant material and Kan Nobuta and Gayathri Mahalingam for assistance with the computational methods..


title: High-throughput sequencing of small RNAs in Panicum virgatum

summary: Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Panicum virgatum tissues (including leaves, drought-treated leaves and flowers). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the maize genome under study.

overall_design: Small RNA libraries were derived from  leaves, drought-treated leaves and flowers of Panicum virgatum. Total RNA was isolated using the Plant RNA Purification Reagent (Invitrogen), and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Pamela Green  for providing the plant material as well as Kan Nobuta and Gayathri Mahalingam for assistance with the computational methods.


title: High-throughput sequencing of small RNAs in Persea americana

summary: Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Persea americana tissues (including leaves, flowers and fruit). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the maize genome under study.

overall_design: Small RNA libraries were derived from  leaves, flowers and fruit of Persea americana. Total RNA was isolated using the Plant RNA Purification Reagent (Invitrogen), and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Doug Soltis  for providing the plant material as well as Kan Nobuta and Gayathri Mahalingam for assistance with the computational methods.


title: High-throughput sequencing of small RNAs in Citrus sinensis

status: Public on Apr 30 2011

summary: Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Citrus sinensis tissues (including leaves, flowers and fruit). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features, such as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the maize genome under study.

overall_design: Small RNA libraries were derived from  leaves, flowers and fruit of Citrus sinensis. Total RNA was isolated using the TriReagent (Molecular Research Center) for leaves and flowers and the Guanidinium-free for fruits, and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Erik Mirkov  for providing the plant material, as well as Kan Nobuta and Gayathri Mahalingam for assistance with the computational methods.


title: High-throughput sequencing of small RNAs in Amborella trichopoda

summary: Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Amborella trichopoda leaves. The high depth of the resulting datasets enabled us to examine in detail critical small RNA features such as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the maize genome under study.

overall_design: A small RNA library was derived from leaves of Amborella trichopoda. The tissue represented a mixture of developmental stages, with a bias towards those from early, actively differentiating cells.  Total RNA was isolated using the TriReagent (Molecular Research Center) and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA library was sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Doug Soltis and AndrÃ© Chanderbali for providing the plant material, as well as Kan Nobuta and Gayathri Mahalingam for assistance with the computational methods.


title: High-throughput sequencing of small RNAs in Hordeum vulgare

summary: Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from different Hordeum vulgare tissues  (leaves, inflorescence and leaves inoculated with Blumeria). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the maize genome under study.

overall_design: Small RNA libraries were derived from leaves, inflorescence and leaves inoculated with Blumeria of Hordeum vulgare. Each tissue represented a mixture of developmental stages. Total RNA was isolated using the Plant RNA Purification Reagent (Invitrogen) and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Roger Wise for providing the plant material and Kan Nobuta and Gayathri Mahalingam for assistance with the computational methods..


title: High-throughput sequencing of small RNAs in Cucurbita maxima

summary: Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Cucurbita maxima tissues (including leaves, flowers and phloem sap). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the maize genome under study.

overall_design: Small RNA libraries were derived from  leaves, flowers and phloem sap of Cucurbita maxima, variety Big Max. Total RNA was isolated using the TriReagent (Molecular Research Center) for leaves and phloem sap and the Plant RNA Purification Reagent (Invitrogen) for flowers, and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Pamela Green  for providing the plant material as well as Kan Nobuta and Gayathri Mahalingam for assistance with the computational methods.


title: PiceaGenExpress database of transcription profiles

status: Public on Feb 08 2012

summary: A small database of transcription profiles called PgGenExpress was developed from over 150 hybridizations spanning eight major tissue types. In total, transcripts were detected for 92% of the genes on the microarray, in at least one tissue. Non-annotated genes were predominantly expressed at low levels in fewer tissues than genes of known or predicted function. Diversity of expression within gene families may be rapidly assessed from PgGenExpress. In conifer trees, dehydrins and late embryogenesis (LEA) osmotic regulation proteins occur in large gene families compared to angiosperms. Strong contrasts and low diversity was observed in the dehydrin family, while diverse patterns suggested a greater degree of diversification among LEAs.

sample_organism:
Picea abies
Picea glauca

overall_design: This is a one-color meta-analysis of tissues from 5 separate experiments. There are 8 different tissue types. Each tissue is represented by a variable number of slides, each slide being a biological repetition, for a total of 149 slides.

first: Jukka-Pekka

last: Verta

first: Armand

last: Séguin

last: Duval

first: Krystyna

last: Klimaszewska

first: Sannakajsa

last: Velmala

first: Taina

last: Pennanen


title: Genome-wide profiling of miRNAs and other small non-coding RNAs in the Verticillium dahliae inoculated cotton roots

city: Anyang

first: Zujun

last: Yin

state: Henan

address: 38 Huanghe Dadao, Anyang 455000, Henan, China

department: Cotton Research Institute

institute: Chinese Academy of Agricultural Sciences

summary: MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) are short (19â25 nucleotides) non-coding RNA molecules that have large-scale regulatory effects on development and on stress responses in plants.The objective of this study is to investigate the transcriptional profile of miRNAs and other small non-coding RNAs in Verticilliumâinoculated cotton roots. Four small RNA libraries were constructed from mocked and infected roots of two cotton cultured species which are with different Verticillium tolerance (âHai-7124â, Gossypium barbadense L., a Verticillium-tolerant cultivar, and âYi-11â, Gossypium hirsutum L. a Verticillium-sensitive cultivar). The length distribution of obtained small RNA pools was significantly different among libraries. A total of 215 conserved miRNA families were identified in the two cotton species, of them 14 are novel. There were >65 families with different expression between two libraries. We also identified two ta-siRNAs and thousands of endogenous siRNA candidates, and hundred of them exhibited altered expression after inoculation of Verticillium. The profiling of these miRNAs and other small non-coding RNAs lay the foundation for further understanding of small RNAs function in the regulation of Verticillium defence responses in cotton roots.

sample_organism:
Gossypium barbadense
Gossypium hirsutum

platform_organism:
Gossypium barbadense
Gossypium hirsutum

overall_design: Examination of 2 different traetments in 2 cotton types.

first: Fafu

last: Shen