title: A draft map of cis-regulatory sequences in the mouse genome

city: La Jolla

type: Genome variation profiling by high throughput sequencing

summary:
The laboratory mouse is the most widely used mammalian model organism in biomedical research. The 2.6 billion bases of the mouse genome share a high degree of conservation with the human genome, so a thorough annotation of the mouse genome will be of significant value to understanding the function of the human genome. To date, most of the functional sequences in the mouse genome have yet to be found, and the cis-regulatory sequences in particular are still poorly annotated.  Comparative genomics has been a powerful tool for the discovery of these sequences, but it alone cannot resolve their temporal and spatial functions.  Recently, ChIP-Seq has been developed to identify cis-regulatory elements in the genomes of several organisms including human, D. melanogaster and C. elegans.  We have applied the same experimental approach to a diverse set of 19 tissues and cell types in the mouse, producing a map of nearly 300,000 murine cis-regulatory sequences. This map provides functional annotation to nearly 11% of the mouse genome, and over 70% of conserved, non-coding sequences (CNS). We define tissue-specific enhancers and identify potential transcription factors regulating gene expression in each tissue or cell type. Finally, we demonstrate that much of the mouse genome is organized into domains of coordinately regulated enhancers and promoters. Our results provide a resource for the annotation of functional elements in the mammalian genome and study of mechanisms regulating tissue-specific gene expression.

This SuperSeries is composed of the SubSeries listed below.

overall_design: 19 tissues and primary cell types were examined using ChIP-Seq, RNA-Seq. Additionally we performed HiC experiments in mouse cortex.


title: Spi-1/PU.1 activates transcription through clustered DNA occupancy in erythroleukemia

status: Public on Jun 30 2012

city: Zurich

first: Valentina

last: Boeva

address: Universitatstrasse 6

department: Computer Science

country: Switzerland

institute: ETH Zurich

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Acute leukemia are characterized by deregulation of transcriptional networks that control the lineage specificity of gene expression. The aberrant overexpression of the Spi-1/PU.1 transcription factor leads to erythroleukemia. To determine how Spi-1 mechanistically influences the transcriptional program, we combined a ChIP-seq analysis with transcriptional profiling in cells from an erythroleukemic mouse model. We show that Spi-1 displays a selective DNA-binding that does not often cause transcriptional modulation. We report that Spi-1 controls transcriptional activation and repression through distinct Spi-1 recruitment to chromatin. We revealed several parameters impacting on Spi-1-mediated transcriptional activation. Gene activation is facilitated by Spi-1 occupancy close to transcriptional starting site of genes devoid of CGIs. Moreover, in those regions Spi-1 acts by binding to multiple motifs tightly clustered and with similar orientation. Finally, in contrast to the myeloid and lymphoid B cells in which Spi-1 exerts a physiological activity, in the erythroleukemic cells, lineage-specific cooperating factors do not play a prevalent role in Spi-1-mediated transcriptional activation. Thus, our work describes a new mechanism of gene activation through clustered site occupancy of Spi-1 particularly relevant in regard to the strong expression of Spi-1 in the erythroleukemic cells.

overall_design: Chromatin immunoprecipitations of Spi-1, H3K36me3, RNApolII,mouse IgG followed by  sequencing were performed on spleen-derived erythroleukemic cells of spi-1 transgenic mice. In case of Spi-1, reads obtained from the two different mice represent biological replicates and were merged for bioinformatic analysis. Input DNA from each ChIP experiments  have been  pooled and sequenced as one control.

first: Maya

last: Ridinger-Saison

first: Pauline

last: Rimmelé

first: Ivan

last: Kulakovskiy

first: Isabelle

last: Gallais

first: Benjamin

last: Levavasseur

first: Caroline

last: Paccard

first: Patricia

last: Legoix-Né

first: Philippe

last: Hupé

first: François

last: Morlé

first: Alain

last: Nicolas

first: Emmanuel

last: Barillot

first: Françoise

last: Moreau-Gachelin

first: Christel

last: Guillouf


title: Epigenome analysis of normal and IPF lung tissue samples

city: Birmingham

first: Yan

last: Sanders

state: AL

address: 901 19th Street S

country: USA

institute: University of Alabama at Birmingham

summary: Genome wide DNA methylation profiling of normal and IPF lung samples. The Illumina human methylation 27 Beadchip was used to obtain DNA methylation profiles across approximately 27,000 CpGs samples. 2 normal samples, and 4 IPF samples

overall_design: Bisulphite converted DNA from the 12 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2


title: RBFOX1 Splicing and Transcriptional Regulation in Neurons

status: Public on Jun 29 2012

city: Los Angeles

first: Brent

middle: L

last: Fogel

state: CA

address: 710 Westwood Plaza

department: Neurology

institute: UCLA

type: Expression profiling by high throughput sequencing

summary: We used RNA sequencing to identify the RBFOX1 splicing network at a genome-wide level in primary human neural stem cells during differentiation. We observe that RBFOX1 regulates a large set of alternative splicing events implicated in neurogenesis and cell maintenance. Subsequent alterations in gene expression define an additional transcriptional network regulated by RBFOX1 involved in neurodevelopmental pathways remarkably parallel to those affected by splicing.

overall_design: RNA sequencing at a 75bp single-end read scale was performed using polyA-enriched RNA from 5 biological replicates of primary human neural progenitor cell lines generated by lentiviral-mediated knockdown of GFP (control) or RBFOX1 and differentiated for 4 weeks.

first: Eric

last: Wexler

first: Tara

last: Friedrich

first: Genevieve

last: Konopka

first: Daniel

middle: H

last: Geschwind


title: RNA-Seq Analysis Reveals Different Dynamics of Differentiation of Human Dermis- and Adipose-derived Stromal Stem Cells

status: Public on Jun 28 2012

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 2

department: MBB

country: Sweden

institute: Karolinska Institutet

summary: Background: Tissue regeneration and recovery in the adult body depends on self-renewal and differentiation   of stem and progenitor cells. Mesenchymal stem cells (MSCs) that have the ability to   differentiate into various cell types, have been isolated from the stromal fraction of virtually all   tissues. However, little is known about the true identity of MSCs. MSC populations exhibit great   tissue-, location- and patient-specific variation in gene expression and are heterogeneous in cell   composition.   Methodology/Principal findings: Our aim was to analyze the dynamics of differentiation of two closely related stromal cell types,   adipose tissue-derived MSCs and dermal fibroblasts (FBs) along adipogenic, osteogenic and   chondrogenic lineages using multiplex RNA-seq technology. We found that undifferentiated   donor-matched MSCs and FBs are distinct populations that stay different upon differentiation   into adipocytes, osteoblasts and chondrocytes. The changes in lineage-specific gene expression   occur early in differentiation and persist over time in both MSCs and FBs. Further, MSCs and   FBs exhibit similar dynamics of adipogenic and osteogenic differentiation but different dynamics   of chondrogenic differentiation.  Conclusion: Our findings suggest that stromal stem cells including adipose-derived MSCs and dermal FBs   exploit different molecular mechanisms of differentiation to reach a common cell fate. The early   mechanisms of differentiation are lineage-specific and are similar for adipogenic and osteogenic   differentiation but are distinct for chondrogenic differentiation between MSCs and FBs.

overall_design: A total of 91 samples were analyzed by multiplex RNA-seq. Samples represented replicates from two patients, two cell types and three differentiation protocols, as indicated by the sample annotation. 5 barcodes were unused, but the corresponding FASTQ files are included for completeness.

first: Kersti

last: Jääger

first: Saiful

last: Islam

first: Pawel

last: Zajac

first: Toomas

last: Neuman


title: Dorsal dependent CBP binding on a genome wide scale

first: Mattias

last: Mannervik

address: Arrheniuslaboratories E3

department: Molecular Biosciences, the Wenner-Gren Institute

institute: Stockholm University

summary: We find a high concordance between the binding of the Drosophila transcription factor Dorsal and the co-activator CBP during early embryogenesis. This relationship was furter examined by comparing CBP distribution in Drosophila embryos derived from wt and mutant flies lacking intranuclear Dorsal (gd7). Our data suggests a specific involvemet of CBP in initiating early dorsoventral patterning, but not in anterioposterior.

overall_design: CBP ChIP seq of 2-4 hours old Drosophila embryos derived from w1118 (wild-type) or gd7 homozygous mutant mothers

first: Per-Henrik

last: Holmqvist

first: Ann

last: Boija

first: Philige

last: Philip

first: Filip

last: Crona

first: Per

last: Stenberg


title: Major concepts of piRNA biogenesis revealed by the analysis of Shutdown, a co-chaperone with essential roles in the biogenesis of all Drosophila piRNA populations

city: Vienna

first: Julius

last: Brennecke

address: Dr. Bohrgasse 3

country: Austria

institute: IMBA

type: Non-coding RNA profiling by high throughput sequencing

summary: In animal gonads, 23-30nt long PIWI interacting RNAs (piRNAs) guarantee genome integrity by guiding the sequence specific silencing of selfish genetic elements such as transposons. Two major branches of piRNA biogenesis, namely primary processing and ping-pong amplification, feed into the PIWI clade of Argonaute proteins. Despite our conceptual understanding of piRNA biogenesis, major gaps exist in the mechanistic understanding of the underlying molecular processes as well as in the knowledge of the involved players. Here, we demonstrate an essential role for the female sterility gene shutdown in the piRNA pathway. Shutdown, an evolutionarily conserved co-chaperone of the immunophilin class is the first piRNA biogenesis factor that is essential for all primary and secondary piRNA populations in Drosophila. Based on these findings, we define distinct groups of piRNA biogenesis factors and reveal the core concept of how PIWI family proteins are hard-wired into piRNA biogenesis processes.

overall_design: small-RNA libraries from 2 control samples and 7 knock-down samples of D. mel. ovaries and 2 small-RNA profiles from Piwi IP and Aub IP from OSCs.

last: Olivieri


title: Transcriptional profiling of a novel mutant resistant to imidacloprid and DDT

city: Belgrade

first: Predrag

middle: M

last: Kalajdzic

address: Despota Stefana 142

department: Department for population genetics and ecogenotoxicology

country: Serbia

institute: Institute for biological research "Sinisa Stankovic"

summary: Deep-sequencing analysis of mRNA expression differences between imidacloprid and DDT resistant mutant line and iso31 (w1118) susceptible line have been obtained. A total of 357 transcripts were found to be differently expressed, with 150 upregulated and 207 downregulated genes in the resistant line.

overall_design: Analysis of poly(A)+ RNA from one resistant mutant and one iso31 (w1118) susceptible (control) sample

first: Charalambos

last: Savakis

first: Ioannis

last: Ragoussis

first: Martin

last: Reczko

first: Artemis

last: Hatzigeorgiou


title: Analysis of a normalised equine cDNA library using deep sequencing

city: Neuherberg

first: Brigitte

last: Waegele

address: Ingolstädter Landstr. 1

country: Germany

institute: Helmholtz Zentrum München

summary:
While a first draft of the equine genome is available and predictions are made regarding resulting genes and proteins, little is known about the actual transcriptome. So far, published expressed sequence tags (ESTs) from different horse tissues were generally rather short (≤600bp) and hardly annotated, reflecting the problem that good cDNA libraries are very difficult to analyse. In this approach, we aimed to establish and analyse a normalised immune cell cDNA library (using freshly isolated and activated lymphocytes, NK cells, monocytes and DC). In particular, we wanted to test next generation sequencing combined with a series of bioinformatic approaches.
The resulting cDNA library contained 2x107 clones of which 1056 were used for an initial Sanger sequencing and 4x106 for the deep sequencing analysis. Through the latter we obtained >29k sequences for which more than 5000 matches where found on the equine reference sequences. Additionally we could identify more than 3500 sequences which had matches on both - non-equine RNA sequences  as well as the equine genome. In these we find both extensions of existing RefSeq models and novel mRNAs alike. Less than 2% of sequences did not have any match in the mentioned databases.

overall_design: 1 pooled set of samples from one animal analysed

first: Berthold

last: Farthmann

first: Gerald

last: Nyakatura

first: Dagmar

last: Heubner

first: Hans-Werner

last: Mewes

first: Falko

last: Steinbach


title: Identification and characterization of small non-coding RNAs from Chinese fir by high throughput sequencing

city: Beijing

first: Jinxing

last: Lin

address: No.20 Nanxincun, Xiangshan

country: China

institute: Institute of botany

summary: Small non-coding RNAs (sRNAs) play key roles in plant development, growth and responses to biotic and abiotic stresses. At least four classes of sRNAs have been well characterized in plants, including repeat-associated siRNAs (rasiRNAs), microRNAs (miRNAs), trans-acting siRNAs (tasiRNAs) and natural antisense transcript-derived siRNAs. Chinese fir (Cunninghamia lanceolata) is one of the most important coniferous evergreen tree species in China. No sRNA from Chinese fir has been described to date. To obtain sRNAs in Chinese fir, we sequenced a sRNA library generated from seeds, seedlings, leaves, stems and calli, using Illumina high throughput sequencing technology. A comprehensive set of sRNAs were acquired, including conserved and novel miRNAs, rasiRNAs and tasiRNAs. With BLASTN and MIREAP we identified a total of 115 conserved miRNAs comprising 40 miRNA families and one novel miRNA with precursor sequence. The expressions of 16 conserved and one novel miRNAs and one tasiRNA were detected by RT-PCR. Utilizing real time RT-PCR, we revealed that four conserved and one novel miRNAs displayed developmental stage-specific expression patterns in Chinese fir. In addition, 209 unigenes were predicted to be targets of 30 Chinese fir miRNA families, of which five target genes were experimentally verified by 5' RACE, including a squamosa promoter-binding protein gene, a pentatricopeptide (PPR) repeat-containing protein gene, a BolA-like family protein gene, AGO1 and a gene of unknown function. We also demonstrated that the DCL3-dependent rasiRNA biogenesis pathway, which had been considered absent in conifers, existed in Chinese fir. Furthermore, the miR390-TAS3-ARF regulatory pathway was elucidated.  We unveiled a complex population of sRNAs in Chinese fir through high throughput sequencing. This provides an insight into the composition and function of sRNAs in Chinese fir and sheds new light on land plant sRNA evolution.

overall_design: The aim of this study is to investigate the small RNA transcriptome in Cunninghamia lanceolata. Total RNAs of seeds and calli were extracted using RNAiso-mate for plant tissue and RNAiso plus (Takara, Dalian, Liaoning, China), whereas total RNAs of seedlings, adult leaves and stems were isolated with the Concert Plant RNA Reagent (Invitrogen, Carlsbad, CA, USA), and were then treated with RNase-free DNase I (Promega, Madison, WI, USA). Equal amount of total RNAs from the 5 different samples were mixed to form a single RNA pool. Twenty micrograms of total RNAs from the pool were used and 16 to 30-nt sRNAs were purified using Novex 15% TBE-¬Urea gel (Invitrogen). Two adaptors were sequentially ligated to the 5' and 3' ends of purified sRNAs. The ligation products were further purified from Novex 10% TBE-Urea gel. Reverse transcriptase SuperScript II (Invitrogen) and high-fidelity DNA polymerase Phusion (New England Biolabs, Ipswich, MA, USA) were used in the following RT-PCR reaction. The amplification products were cut from Novex 6% TBE-Urea gel. The purified DNA fragments were used for sequencing on an Illumina 1G Genome Analyzer at the Beijing Genomics Institute, Shenzhen, China.

first: Lichuan

last: Wan

first: Feng

last: Wang

first: Xiangqian

last: Guo

first: Yuanyuan

last: Zhao

first: Haiyan

last: Zhang


title: Genome wide profiling of PAX8 binding stes in PCCL3 rat cells

city: Madrid

first: Pilar

last: Santisteban

state: Madrid

address: Arturo Duperier 4

department: Physiopathology of the Endocrine and Nervous System

country: Spain

institute: Biomedical Research Institute-CSIC

summary: Analysis of PAX8 binding sites by chromatin immunoprecipitation coupled with ultra-high-throughput sequencing (ChIP-seq) in PCCL3 rat cells. Results provide insight into the contribution of this regulatory factor to transcription genome-wide.

overall_design: We generate a genome wide map of PAX8 binding sites in PCCL3 cells using as negative control an input DNA obtained just prior to Pax8 immunoprecipitation

first: Sergio

last: Ruiz-Llorente

first: Enrique

last: Carrillo-de Santa Pau

first: C

last: Montero-Conde

first: Gonzalo

last: Gomez-Lopez

first: J

middle: A

last: Fagin

first: Alfonso

last: Valencia

first: David

middle: G

last: Pisano


title: Brassinosteroid, gibberellin, and phytochrome impinge on a common transcription module in Arabidopsis

status: Public on Jun 25 2012

city: Jinan

first: Mingyi

last: Bai

state: Shandong

address: 27 Shandananlu

department: Life of Scienec

institute: Shandong University

summary: Brassinosteroid (BR) and gibberellin (GA) promote many similar developmental responses in plants; but their relationship remains unclear. Here we show that BR and GA act interdependently through a direct interaction between the BR-activated BZR1 and GAinactivated DELLA transcription regulators. GA promotion of cell elongation required BR signaling, whereas BR or active BZR1 can suppresssed the GA-deficient dwarf phenotype. DELLAs directly interacted with BZR1 and inhibited BZR1-DNA binding both in vitro and in vivo. Genome-wide analysis defined a BZR1-dependent GA-regulated transcriptome, which is enriched with light-regulated genes and genes involved in cell wall synthesis and photosynthesis/chloroplast. GA promotion of hypocotyl elongation requires both BZR1 and the phytochrome interacting factors (PIFs), as well as their common downstream targets PREs. The results demonstrate that GA releases DELLA-mediated inhibition of BZR1, and that the DELLA-BZR1-PIF4 interaction defines a core transcription module that mediates coordinated growth regulation by GA, BR and light signals.

overall_design: Wild type Arabidopsis and bzr1-1D were grown in media containing 1 μM PAC and 0 or 2 μM PPZ for 4.5 days in dark, then treated with 10 μM GA3 or mock solution for 12 hr. Total RNA was extracted with Spectrum Plant Total RNA Kit (Sigma) and the mRNA sequencing libraries were constructed with barcodes using TruSeqTM RNA Sample Preparation Kit (Illumina). Six barcoded libraries were pooled together and sequenced by Illumina HiSeq2000.

first: Zhiyong


title: Targeted RT-PCR assays spanning unannotated splice junctions sequenced by Roche 454.

status: Public on Jun 26 2012

city: Barcelona

first: Julien

last: Lagarde

address: Dr. Aiguader 88

department: Bioinformatics and Genomics

institute: CRG

summary:
The ENCODE projects seeks to identify and characterize functional elements in the human genome.  Throughout the scale-up phase of ENCODE, the transcriptome group has generate Long RNA-Seq, Small RNA-Seq, Cap-Analysis of Gene Expression (CAGE), and RNA-PET short read data on the Illumina platform for ~ 40 different human primary and transformed cell lines in replicate.   From these data several high-resolution and discrete features/elements have been mined out (5’ caps, splice junctions, polyadenylation sites, small RNAs, etc…).  However, because these data are obtained from short-read data, we have only limited “connectivity” information.  For example, from the long RNA-Seq data, which was sequenced in mate-pair fashion with average insert sizes ~ 200 bp, we know that the sequence from mate 1 is physically linked to the sequence in mate 2.  We don’t know the sequence in between and we don’t know how this mate-pair is connected to other mate-pairs in the context of longer transcripts in vivo.  To date, this information is gleaned from models generated in silico: In our case, by the program Cufflinks.  Consequently, we have a collection of transcript models exhibiting a vast array of local complexity assembled from short read data that need to be experimentally tested.  Alternatively, one can “cut to the chase” and use a more raw/elemental form of the data as a basis for additional experimentation to clone out the longer sequences generated in vivo.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: 454 Data from HepG2, HUVEC, and H1 ES cells

first: T

last: Gingeras

last: Davis


title: Intracellular and  extracellular microRNAs expressed by HEK293T cells

city: Belfast

middle: Arthur

last: Simpson

state: N. Ireland

address: QUB Institue of clinical Science, Block A, RVH

department: Centre for Experimental Medicine

country: United Kingdom

institute: Queen's University Belfast

summary: MicroRNAs (miRNAs) are a class of small RNA molecules that regulate expression of specific mRNA targets. They can be released from cells, often encapsulated within extracellular vesicles (EVs), and therefore have the potential to mediate intercellular communication. It has been suggested that certain miRNAs may be selectively exported, although the mechanism has yet to be identified. Manipulation of the miRNA content of EVs will be important for future therapeutic applications. We therefore wished to assess which endogenous miRNAs are enriched in EVs and how effectively an overexpressed miRNA would be exported. Small RNA libraries from HEK293T cells and vesicles before or after transfection with a vector for miR-146 overexpression were analysed by deep sequencing. A subset of miRNAs was found to be enriched in EVs. The global expression data provided by deep sequencing confirms that specific miRNAs are enriched in EVs released by HEK293T cells.

overall_design: Cells were transfected with a plasmid to direct overexpression of miR-146a. Extracellular vesicles were isolated by ultracentrifugation from untreated and transfected cells. RNA was isolated from one sample each of untreated and transfected cells and vesicles.Small RNA libraries were prepared for sequencing.


title: Global analysis of in vivo Pax8-binding sites in rat thyroid cells using high-throughput technologies: Chip-Seq and whole genome expression arrays

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

overall_design: Refer to individual Series


title: Transcriptome dynamics during fruit development of sweet orange (Citrus sinensis)

status: Public on Jun 22 2012

city: Ithaca

first: Qiang

last: Xu

state: NY

address: Tower Road, Cornell University

institute: Cornell University

summary: • To dissect how the genes are dynamically and differentially expressed during fruit development in sweet orange, a comprehensive transcriptomic study was performed in a pleiotropic mutant (MT) and its wild type (WT).  • The detection of the fruit transcriptomic changes was conducted at five stages of fruit development by deep sequencing; the obtained millions of reliable tags were mapped on orange unigenes and subjected to cluster analysis and functional categorization. Sugar and organic acid contents were determined based on the prediction of differential biological processes.  • The global clustering analysis revealed a total of 14 expression patterns for the genes involved in fruit development of sweet orange. More than 94% of the genes showed differential expression during fruit development. Comparative transcripts profiling between WT and MT revealed that between 410 and 634 genes were significantly differentially expressed at the five stages. Functional categorization indicated that TCA cycle, carotenoid biosynthesis, and pentose phosphate pathway (OPP) were among the most regulated pathways.   • This study provided a dynamic-view of the transcriptome changes during fruit ripening in sweet orange; the results highlighted a set of molecular processes involved in the formation of the mutation trait in the orange fruits.

overall_design: Investigate the transcriptome changes during five fruit developmental stages of two sweet orange genotypes

first: Xiuxin

last: Deng


title: Transcriptomic analysis of the stress response to weaning at housing in bovine leukocytes using RNA-seq technology

city: Dunsany

middle: J

last: Lynn

address: Grange

department: Animal & Bioscience

country: Ireland

institute: Teagasc

summary:
Background: Weaning of beef calves is a necessary husbandry practice and involves separating the calf from its mother, resulting in numerous stressful events including dietary change, social reorganisation and the cessation of the maternal-offspring bond and is often accompanied by housing. While much recent research has focused on the physiological response of the bovine immune system to stress in recent years, little is known about the molecular mechanisms modulating the immune response. Therefore, the objective of this study was to provide new insights into the molecular mechanisms underlying the physiological response to weaning at housing in beef calves using Illumina RNA-seq.

Results: The leukocyte transcriptome was significantly altered for at least 7 days following either housing or weaning at housing. Analysis of differentially expressed genes revealed that four main pathways, cytokine signalling, transmembrane transport, haemostasis and G-protein-coupled receptor (GPRC) signalling, were differentially regulated between control and weaned calves and underwent significant transcriptomic alterations in response to weaning stress on day 1, 2 and 7. Of particular note, chemokines, cytokines and integrins were consistently found to be up-regulated on each day following weaning. Evidence for alternative splicing of genes was also detected, indicating that a number of genes involved in the innate and adaptive immune response may be alternatively transcribed, including those responsible for toll receptor cascades and T cell receptor signalling.

Conclusions: This study represents the first application of RNA-Seq technology for genomic studies in bovine leukocytes in response to weaning stress. Weaning stress induces the activation of a number of cytokine, chemokine and integrin transcripts and may alter the immune system whereby the ability of a number of cells of the innate and adaptive immune system to locate and destroy pathogens is transcriptionally enhanced. Stress alters the homeostasis of the transcriptomic environment of leukocytes for at least 7 days following weaning, indicating long-term effects of stress exposure in the bovine. The identification of gene signature networks that are stress activated provides a mechanistic framework to characterise the multifaceted nature of weaning stress adaptation in beef calves. Thus, capturing subtle transcriptomic changes provides insight into the molecular mechanisms that underlie the physiological response to weaning stress.

overall_design:
Examination of a time course (day 0, 1, 2 and 7) for 2 treatments, calves either housed with their dam (control) or housed and simultaneously weaned, using RNA-seq.

The supplementary processed data file 'read_counts.txt' contains unnormalized read counts for each Ensembl bovine gene in each of the 48 samples. Unnormalized counts are required for input to EdgeR.
Genome build: Btau4.0

first: Aran

last: O'Loughlin

first: Mark

last: McGee

first: Sean

last: Doyle

first: Matthew

last: McCabe

first: Bernadette

last: Earley


title: Genome-wide occupancy profile of Tbx3, Gata4, Nkx2-5 and p300 in adult mouse whole heart

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

country: Netherlands

institute: Amsterdam UMC

summary: The contraction pattern of the heart relies on the activation and conduction of the electrical impulse. Perturbations of cardiac conduction have been associated with congenital and acquired arrhythmias as well as cardiac arrest. The pattern of conduction depends on the regulation of heterogeneous gene expression by key transcription factors and transcriptional enhancers. Here, we assessed the genome-wide occupation of conduction system–regulating transcription factors TBX3, NKX2-5, and GATA4 and of enhancer-associated coactivator p300 in the mouse heart, uncovering cardiac enhancers throughout the genome.

overall_design: Examination of 3 cardiac transcription factors and p300 in adult mouse heart

first: Malou

last: van den Boogaard

first: Phil

last: Barnett


title: Biased transcription and selective degradation of small RNAs shape the pattern of DNA elimination in Tetrahymena

status: Public on Jun 21 2012

city: Montpellier

first: Kazufumi

last: Mochizuki

address: 141 rue de la Cardonille

country: France

institute: Institute of Human Genetics, CNRS

summary: The ciliated protozoan Tetrahymena undergoes extensive programmed DNA elimination when the germline micronucleus produces the new macronucleus during sexual reproduction. DNA elimination is epigenetically controlled by DNA sequences of the parental macronuclear genome, and this epigenetic regulation is mediated by small RNAs (scnRNAs) of approximately 28-30 nucleotides that are produced and function by an RNAi-related mechanism. Here, we examine scnRNA production and turnover by deep sequencing. scnRNAs are produced exclusively from the micronucleus and non-homogeneously from a variety of chromosomal locations. scnRNAs are preferentially derived from the eliminated sequences, and this preference is mainly determined at the level of transcription. Despite this bias, a significant fraction of scnRNAs is also derived from the macronuclear-destined sequences, and these scnRNAs are degraded during the course of sexual reproduction. These results indicate that the pattern of DNA elimination in the new macronucleus is shaped by the biased transcription in the micronucleus and by the selective degradation of scnRNAs in the parental macronucleus.

overall_design: GRO-Seq and Examination of siRNAs in wild-type,nullisomic 4,  EMA1 KO, and TWI1 KO Tetrahymena cells

first: Ursula

middle: E

last: Schoeberl

first: Henriette

last: Kurth

first: Tomoko

last: Noto


title: Genome-wide characterization of long nonpolyadenylated RNAs

status: Public on Jul 01 2012

city: Shanghai

first: Ling-Ling

last: Chen

address: 320 Yue-Yang Road

institute: Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

summary: We have used deep sequencing to explore the repertoire of both poly(A)+ and poly(A)- RNAs from two standard cell lines, HeLa cells and human embryonic stem cell (hESC) H9 cells.

overall_design: Examination of nonpolyadenylated and polyadenylated RNA in 2 cell types.

first: Ling

first: Li

last: Yang

first: Michael

middle: O

last: Duff

first: Brenton

middle: R

last: Graveley

first: Goardon

last: Carmichael


title: Genome-wide microRNA expression analysis of clear cell Renal Cell Carcinoma by next generation deep sequencing

city: Leiden

first: Henk

last: Buermans

state: ZH

address: Albinusdreef 2

department: Human Genetics

institute: Leiden University Medical Center

summary: MicroRNAs (miRNAs), non-coding RNAs regulating gene expression, are frequently aberrantly expressed in human cancers. Next-generation deep sequencing technology enables genome-wide expression profiling of known miRNAs and discovery of novel miRNAs at unprecedented quantitative and qualitative accuracy.   Deep sequencing was performed on 22 fresh frozen clear cell renal cell carcinoma (ccRCC), 11 non-tumoral renal cortex (NRC) samples and 2 ccRCC cell lines (n=35). The 22 ccRCCs patients belonged to 3 prognostic sub-groups, i.e. Those without disease recurrence, with recurrence and with metastatic disease at diagnosis

overall_design: Deep sequencing was performed on 22 fresh frozen clear cell renal cell carcinoma (ccRCC), 11 non-tumoral renal cortex (NRC) samples and 2 ccRCC cell lines (n=35). The 22 ccRCCs patients belonged to 3 prognostic sub-groups, i.e. Those without disease recurrence, with recurrence and with metastatic disease at diagnosis.

first: Susanne

last: Osanto

first: Yongjun

last: Qin

middle: P

first: Joost

last: Berkers

first: Evelyne

last: Lerut

first: Jelle

last: Goeman

first: Hendrik

last: van Poppel


title: Extensive conservation of ancient microsynteny across metazoans

city: Darlinghurst

first: Ozren

last: Bogdanovic

state: NSW

address: 384 Victoria Street

department: Genomics and Epigenetics

country: Australia

institute: Garvan Institute of Medical Research

summary: Gene order, or microsynteny, is generally thought not to be conserved across metazoan phyla. Only a handful of exceptions, typically of tandemly duplicated genes such as Hox genes, have been discovered. Here, we performed a systematic survey for microsynteny conservation in 17 genomes and identified nearly 600 pairs of unrelated genes that have remained together across over 600 million years of evolution. Using multiple genome-wide resources, including several genomic features, epigenetic marks, sequence conservation and microarray expression data, we provide extensive evidence that many of these ancient microsyntenic arrangements have been conserved in order to preserve either (i) the coordinated transcription of neighboring genes, or (ii) Genomic Regulatory Blocks (GRBs), in which transcriptional enhancers controlling key developmental genes are contained within nearby “bystander” genes. In addition, we generated ChIP-seq data for key histone modifications in zebrafish embryos to further investigate putative GRBs in embryonic development. Finally, using chromosome conformation capture (3C) assays and stable transgenic experiments, we demonstrate that enhancers within bystander genes drive the expression of genes such as Otx and Islet, critical regulators of central nervous system development across bilaterians. These results show that ancient genomic associations are far more common in modern metazoans than previously thought – likely involving over 12% of the ancestral bilaterian genome – and that cis-regulatory constraints have played a major role in conserving the architecture of metazoan genomes.

overall_design: ChIP-seq H3K27me3 of 24hpf  zebrafish embryos

first: Manuel

last: Irimia

first: Maria

middle: S

last: Alexis

first: Ana

last: Fernandez-Miñan

first: Ignacio

last: Maeso

last: Bogdanović

first: Elisa

last: de la Calle-Mustienes

first: Scott

middle: W

last: Roy

first: José

last: Gómez-Skarmeta

first: Hunter

middle: B

last: Fraser


title: Fcp1 dephosphorylation of the RNA polymerase II C-terminal domain required for efficient transcription of heat shock genes

first: Nicholas

last: Fuda

state: New York

address: 417 Biotechnology Building, Cornell University

department: Molecular Biology and Genetics

summary: RNA polymerase II is decreased on heat shock-induced genes when the CTD phosphatase Fcp1 is knocked down in Drosophila S2 cells. We examined transcriptionally-engaged Pol II genome-wide with GRO-seq to determine if other genes are similarly affected.

overall_design: Two biological replicates of nascent RNA sequencing

first: John

middle: T

last: Lis


title: Nanoarchaeum equitans small RNA analysis

status: Public on Jun 20 2012

city: Marburg

first: Lennart

last: Randau

address: Karl-von-Frisch Strasse 10

institute: MPI for terrestrial microbiology

summary: We report the profiling of small RNAs from Nanoarchaeum equitans by high-throughput sequencing. Over 16 million Illumina HiSeq 2000 reads were mapped to the 490,885-nucleotide small genome of Nanoarchaeum equitans. The mapping allowed the identification of highly abundant C/D box sRNAs and crRNAs in an organism that has to import its nucleotides from Ignicoccus hospitalis. The precursor tRNA halves of trans-spliced tRNAs were identified.

overall_design: Analysis of small RNA from one sample of Nanoarchaeum equitans.


title: Polyglutamine expanded huntingtin dramatically alters the genome-wide binding of HSF1 (ChIP-Seq)

status: Public on Jun 19 2012

city: Cambridge

first: Laura

last: Riva

state: MA

address: 77 Massachusetts Avenue

department: Biological Engineering

institute: MIT

summary: In Huntington’s disease (HD), polyglutamine  expansions in the huntingtin (Htt) protein cause subtle changes in cellular functions that, over-time, lead to neurodegeneration and death. Studies have indicated that activation of the heat shock response can reduce many of the effects of mutant Htt in disease models, suggesting that the heat shock response is impaired in the disease. To understand the basis for this impairment, we have used genome-wide chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-Seq) to examine the effects of mutant Htt on the master regulator of the heat shock response, HSF1. We find that, under normal conditions, HSF1 function is highly similar in cells carrying either wild-type or mutant Htt. However, polyQ-expanded Htt severely blunts the HSF1-mediated stress response. Surprisingly, we find that the HSF1 targets most affected upon stress are not directly associated with proteostasis, but with cytoskeletal binding, focal adhesion and GTPase activity.  Our data raise the intriguing hypothesis that the accumulated damage from life-long impairment in these stress responses may contribute significantly to the etiology of Huntington's disease.

overall_design: ChIP-Seq experiments for HSF-1 were performed in striatal cells that express either wild-type or mutant Htt using ChIP-Seq technology under normal (33°C) and heat shock (42°C for six hours) conditions. The cells were crosslinked with 1% formaldehyde and immunoprecipitated using antibody sc-9144 (Santa Cruz Biotech) for HSF-1. Sequencing was performed using the Illumina Genome Analyzer II.

first: Martina

last: Koeva

first: Ferah

last: Yildirim

first: Leila

last: Pirhaji

first: Deepika

last: Dinesh

first: Tali

last: Mazor

first: Martin

last: Duennwald

first: Ernest

last: Fraenkel


title: Polyglutamine expanded huntingtin dramatically alters the genome-wide binding of HSF1


title: Distribution of histone modificiation H3K27me3 in Drosophila Kc cells, comparison with dCTCF knockdown

status: Public on Jun 18 2012

city: Palo Alto

first: Kevin

last: Van Bortle

address: 3165 Porter Dr

department: Genetics

institute: Stanford University

summary: Here we map the localization of H3K27me3 in Drosophila Kc cells, as well as in Drosophila Kc cells wherein dCTCF is knock down.

overall_design: examination of genomic occupancy for H3K27me3, control samples used for Drosophila Kc were previously described (Wood, Van Bortle et al., 2011 GSE30740)

first: Victor

last: Corces

last: VanBortle

first: Edward

last: Ramos


title: Distribution of Drosophila insulator proteins Mod(mdg4) and L(3)mbt in Kc cells

summary: Here we map the localization of Mod(mdg4), including Mod(mdg4)2.2 specific and Mod(mdg4) common to all isoforms, to chromatin insulators, as well as the lethal-3 malignant brain tumor protein in Drosophila Kc cells.

overall_design: examination of genomic occupancy for Mod(mdg4)2.2, Mod(mdg4)BTB (all isoforms), and L(3)mbt, control samples used for Drosophila Kc were previously described (Wood, Van Bortle et al., 2011 GSE30740)


title: Distinctive profiles of small RNA couple inverted repeat-induced post-transcriptional gene silencing with endogenous RNA silencing pathways in Arabidopsis

city: Davis

first: Richard

last: Michelmore

address: Genome & Biomedical Sciences Facility, 451 East Health Sciences Drive

department: Genome Center

institute: University of California, Davis

summary:
Next-generation Illumina sequencing technology was used to analyze small RNA associated with post-transcriptional gene silencing induced by intron-spliced hairpin RNA (ihpRNA) in Arabidopsis.

The experimental induction of RNA silencing in plants often involves expression of transgenes encoding inverted repeat (IR) sequences to produce abundant dsRNAs that are processed into small RNAs (sRNAs). These sRNAs are key mediators of post-transcriptional gene silencing (PTGS) and determine the specificity of the inhibition of gene expression. Despite its broad utility as a research tool, IR-PTGS is only a partially understood mechanism of RNA silencing in plants. We generated four sets of 60 Arabidopsis plants, each containing IR transgenes expressing different configurations of uidA and CHALCONE SYNTHASE (CHS) gene fragments. The levels of PTGS were dependent on the orientation and position of the fragment in the IR construct. To investigate these differences, we characterized the sRNA profiles by Illumina sequencing of seven libraries generated from transgenic families showing different levels of IR-PTGS. Mapping of sRNA sequences to their corresponding transgene-derived and endogenous transcripts identified distinctive patterns of differential sRNA accumulation. Analyses of these patterns and peaks revealed similarities among sRNAs associated with IR-PTGS and endogenous sRNAs linked to uncapped mRNA decay. We also found unexpected associations between sRNA accumulation and the presence of predicted open reading frames in the trigger sequence. Our observations provide new guidelines for designing constructs to increase the efficiency of IR-PTGS. In addition, strong IR-PTGS affected the prevalence of endogenous sRNAs, which has implications for the use of PTGS for experimental or applied purposes.

overall_design: Sequencing of small RNA from Arabidopsis plants transformed with ihpRNA constructs. Seven small RNA libraries were sequenced: Lib 0, made from non-transgenic Arabidopsis plants, and Libs 1-6, made from plants transformed with different configurations of ihpRNA.

first: Tadeusz

last: Wroblewski

first: Marta

last: Matvienko

first: Urszula

last: Piskurewicz

first: Huaqin

last: Xu

first: Belinda

last: Martineau

first: Joan

last: Wong

first: Alexander

last: Kozik


title: Systems and trans-system level analysis identifies conserved Fe-deficiency responses in the plant lineage

city: Los Angeles

first: Sabeeha

last: Merchant

state: California

address: 607 Charles E. Young Drive East

department: Department of Chemistry and Biochemistry

institute: University of California Los Angeles

summary: We used RNA-Seq to compare the transcriptomes of Fe-replete vs. Fe-deficient vs. Fe-limited Chlamydomonas wild-type cells.  Our RNA-Seq data revealed 90 and 49 genes to be specifically expressed under hetero-phototrophic and phototrophic conditions, respectively. Around 30 genes represent putative Fe-deficiency targets, independent of the carbon source used. Many of these Fe-specific responses are conserved between Chlamydomonas and land plants. We identified several transporters (NRAMP4, a CCC1-like proteins and a ferroportin homologue) all of them most likely being involved in intracellular Fe redistribution. RNA-seq of Chlamydomonas Fe-deficient and limited cells indicated that about 40% of differentially expressed genes represent proteins of unknown functions. Whereas Fe-deficiency gave us insides into putative Fe-specific responses, Fe-limitation revealed responses related to increased oxidative stress. Quantitative proteomics on the soluble Chlamydomonas extracts indicated a fair correlation between changes we detected at mRNA levels compared to changes in protein levels in Fe-deficient and Fe-limited Chlamydomonas. We found that Fe-deficient and Fe-limited cells have increased ascorbate levels, a major antioxidant molecule in plants. Ascorbate levels appear to be elevated by de novo synthesis via the L-Galactose pathway and recycling by monodehydroascorbate reductase. Fe-limited cells showed increased transcript and protein levels of enzymatic antioxidant components of the ascorbate-glutathione scavenging system (MSD3, MDAR1 or GSH1). Fe-limited cells showed the increase of several proteases indicative of elevated proteolitic activity under these severe nutrient limitation conditions.

overall_design: Sampling of Chlamydomonas CC-1021 (2137) cells cultivated photoheterotrophically (TAP) or phototrophically (minimal)  under Fe-replete (20mM), Fe-deficient (1 mM) and Fe-limited (0.25 mM) conditions.

first: Eugen

middle: I

last: Urzica

first: David

last: Casero

first: Hiroaki

last: Yamasaki

first: Scott

last: Hsieh

first: Lital

middle: N

last: Adler

first: Steven

last: Karpowicz

last: Clarke

first: Joseph

last: Loo

first: Matteo

last: Pellegrini


title: Conservation of replication timing reveals global and local regulation of replication origin activity.

city: Norwich

first: Conrad

last: Nieduszynski

address: Norwich Research Park

institute: Earlham Institute

summary: DNA replication initiates from defined locations called replication origins; some origins are highly active whereas others are dormant and rarely used. Origins also differ in their activation time resulting in particular genomic regions replicating at characteristic times and in a defined temporal order. Here we report the comparison of genome replication in four budding yeast species: Saccharomyces cerevisiae, S. paradoxus, S. arboricolus and S. bayanus. First, we find that the locations of active origins are predominantly conserved between species, whereas dormant origins are poorly conserved. Second, we generated genome-wide replication profiles for each of these species and discovered that the temporal order of genome replication is highly conserved. Therefore, active origins are not only conserved in location, but also activation time. Only a minority of these conserved origins show differences in activation time between these species. To gain insight as to the mechanisms by which origin activation time is regulated we generated replication profiles for a S. cerevisiae / S. bayanus hybrid strain and find that there are both local and global regulators of origin function.

sample_organism: Saccharomyces bayanus x Saccharomyces cerevisiae

overall_design:
Measurement of genome replication time from 4 budding yeast species (Saccharomyces cerevisiae, S. paradoxus, S. arboricolus and S. bayanus) and a hybrid (between Saccharomyces cerevisiae and S. bayanus). For each strain two samples were analysed: a replicating sample (from S phase) and a non-replicating sample (from G2 phase)
The reference genome sequences for each yeast species are available as Series supplementary file [sac*.fa]

first: Carolin

last: Müller


title: Genome-wide location analysis of Foxa1 in adult liver

first: Irina

last: Bochkis

address: 7 Cambridge Center

institute: Broad Institute

summary: We determine by genome-wide location analysis (ChIP-Seq) that Foxa1 occupies 5,682 binding sites in the adult murine liver. Although Foxa1 and its closest paralog Foxa2 (GEO accessions: GSE25836 and GSE26729) share a large fraction of binding sites in the liver, each protein also occupies distinct regulatory elements in vivo. Foxa1-only sites have a weaker forkhead motif are enriched for p53 binding sites and are frequently found near genes important to cell cycle regulation, while Foxa2-restricted sites show only a stronger match to the forkhead consensus and are found in genes involved in steroid and lipid metabolism. Thus, Foxa1 and Foxa2, while redundant during development, have evolved divergent roles in the adult liver, ensuring the maintenance of both genes during evolution.

overall_design: 5 biological replicates examined

first: Klaus

middle: H

last: Kaestner


title: RNA-Seq from wt oocytes

city: La Jolla

first: Todd

last: Macfarlan

address: 10010 North Torrey Pines

institute: The Salk Institute

summary: To determine gene expression in mouse ovulated oocytes

overall_design: 3 Replicates of litters of wild type ovulated oocytes

first: Shawn

last: Driscoll


title: mRNA-Seq of 2C::tomato+ vs. - ES cells

summary: We identified/quantified genes and repeat elements enriched within 2C::tomato+ cells vs. 2C::tomato - cells

overall_design: 2C::tomato + and - cells were collected by FACS for RNA-Seq analysis


title: RNA-Seq from wt and G9A knockout ES cells

summary: To measure gene expression difference between wt and g9A knockout ES cells

overall_design: G9A TT2 ES cells (Yokochi et al) were treated with Veh. Or 4OHT (to delete G9A)


title: RNA-Seq from two-cell (2C) stage embryos

summary: To determine gene expression in 2 cell stage embryos

overall_design: 3 Replicates of litters of wild type 2 cell stage embryos


title: 2C::tomato ES cells, 2-cell embryos and wild type oocytes

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

overall_design: Refer to individual Series


title: Global analysis of mRNA decay intermediates in Saccharomyces cerevisiae

status: Public on Jun 17 2012

city: Boulder

first: Yuriko

last: Harigaya

state: Colorado

address: 3415 Colorado Ave, UCB 596

institute: University of Colorado at Boulder

summary: The general pathways of eukaryotic mRNA decay occur via deadenylation followed by 3’ to 5’ degradation or decapping, although some endonuclease sites have been identified in metazoan mRNAs. To determine the role of endonucleases in mRNA degradation in Saccharomyces cerevisiae, we mapped 5’ monophosphate ends on mRNAs in wild-type and dcp2∆ xrn1∆ yeast cells, wherein mRNA endonuclease cleavage products are stabilized. This led to three important observations. First, only few mRNAs that undergo low level endonucleotyic cleavage were observed suggesting that endonucleases are not a major contributor to yeast mRNA decay. Second, independent of known decapping enzymes, we observed low levels of 5’ monophosphates on some mRNAs suggesting that an unknown mechanism can generate 5' exposed ends, although for all substrates tested Dcp2 was the primary decapping enzyme. Finally, we identified debranched lariat intermediates from intron-containing genes, demonstrating a significant discard pathway for mRNAs during the second step of pre-mRNA splicing, which is a potential new step to regulate gene expression.

overall_design: 5' monophosphorylated ends of poly(A) RNA from wild-type and dcp2D xrn1D strains were identified in duplicates and triplicates, respectively.

first: Roy

last: Parker


title: RNA polymerase II pausing downstream of core histone genes is different from genes producing polyadenylated transcripts

status: Public on Jun 15 2012

city: Strasbourg

first: Anamika

last: Krishanpal

address: 1 rue Laurent Fries / BP 10142

institute: Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC)

summary:
Recent genome-wide chromatin immunoprecipitation coupled high throughput
sequencing (ChIP-seq) analyses performed in various eukaryotic organisms, analysed
RNA Polymerase II (Pol II) pausing around the transcription start sites of genes. In this
study we have further investigated genome-wide binding of Pol II downstream of the 3'
end of the annotated genes (EAGs) by ChIP-seq in human cells. At almost all
expressed genes we observed Pol II occupancy downstream of the EAGs suggesting
that Pol II pausing 3' from the transcription units is a rather common phenomenon.
Downstream of EAGs Pol II transcripts can also be detected by global run-on and
sequencing, suggesting the presence of functionally active Pol II. Based on Pol II
occupancy downstream of EAGs we could distinguish distinct clusters of Pol II pause
patterns. On core histone genes, coding for non-polyadenylated transcripts, Pol II
occupancy is quickly dropping after the EAG. In contrast, on genes, whose transcripts
undergo polyA tail addition [poly(A)+], Pol II occupancy downstream of the EAGs can
be detected up to 4-6 kb. Inhibition of polyadenylation significantly increased Pol II
occupancy downstream of EAGs at poly(A)+ genes, but not at the EAGs of core
histone genes. The differential genome-wide Pol II occupancy profiles 3' of the EAGs
have also been confirmed in mouse embryonic stem (mES) cells, indicating that Pol II
pauses genome-wide downstream of the EAGs in mammalian cells. Moreover, in mES
cells the sharp drop of Pol II signal at the EAG of core histone genes seems to be
independent of the phosphorylation status of the C-terminal domain of the large
subunit of Pol II. Thus, our study uncovers a potential link between different mRNA 3'
end processing mechanisms and consequent Pol II transcription termination
processes.

overall_design: Examination of RNA Polymerase II in MCF-7 cell line

first: Gyenis

last: Akos

first: Tora

last: Laszlo


title: RNA-seq profiling of theca and granulosa tissue of dominant follicle at 3 stages of follicular development in cows and heifers.

city: Belfield

first: Paul

last: McGettigan

state: Co Dublin

address: Veterinary Sciences Centre, UCD

department: School of Agriculture, Food Science and Veterinary Medicine

institute: University College Dublin

summary: Cellular mechanisms that contribute to low estradiol concentrations produced by the preovulatory ovarian follicle in cattle with a compromised metabolic status (such as lactatino) are largely unknown. To gain insight into the main metabolic mechanisms affecting preovulatory follicle function RNAseq profiling was conducted on non-lactating Holstein-Friesian heifers (n=16) and lactating Holstein-Friesian cows (n=17) at three stages of preovulatory follicle development: A) newly selected dominant follicle in the luteal phase (Selection); B) follicular phase before the LH surge (Differentiation) and C) pre-ovulatory phase after the LH surge (Luteinization). Based on a combination of RNA sequencing, ingenuity pathway analysis and Q-RT-PCR validation several important molecular markers involved in steroid biosynthesis, such as the expression of steroidogenic acute regulatory protein (STAR) within developing dominant follicles, were identified to be affected (downregulated) by the catabolic state. We propose that the adverse metabolic environment caused by lactation decreases preovulatory follicle function by affecting cholesterol transport into the mitochondria to initiate steroidogenesis.

overall_design: Granulosa and Theca samples from the dominant follicle were taken from cows and heifers at stages: selection, differentiation and luteinization.

first: Siobhan

last: Walsh

first: Jai

last: Mehta

first: John

last: Browne

first: Niamh

last: Forde

first: Radwan

last: Alibrahim

first: Finbar

last: Mulligan

first: Brendan

last: Loftus

first: Mark

last: Crowe

first: Darragh

last: Matthews

first: Michael

last: Diskin

first: Monica

last: Mihm

first: Alexander

middle: C

last: Evans


title: miRNA regulation in the early development of barley seed

status: Public on Jun 16 2012

city: Canberra

first: Jennifer

last: Taylor

address: Clunies Ross St

department: Plant Industry

institute: CSIRO

summary: small RNA and degradome sequencing was carried out on samples isolated from developing barley grains. The datasets were analysed to identify putative miRNAs and their target mRNAs

overall_design: Samples were whole grain tissue (pericarp, embryo and endosperm) from developing barley grains. Three samples were used that pooled 1 to 5, 6-10 and 11-15 days post anthesis grains. For each sample a small RNA library and a degradome library (using the PARE method) was constructed and sequenced using the Illumina platform

first: Julien

last: Curaba

first: Chris

last: Helliwell

middle: M


title: Extensive alternative polyadenylation during zebrafish development

first: Igor

last: Ulitsky

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: The post-transcriptional fate of messenger RNAs (mRNAs) is largely dictated by their 3' untranslated regions (3'UTRs), which are defined by cleavage and polyadenylation (CPA) of pre-mRNAs. We used poly(A)-position profiling by sequencing (3P-Seq) to map poly(A) sites at eight developmental stages and tissues in the zebrafish. Analysis of over 60 million 3P-Seq reads substantially increased and improved existing 3'UTR annotations, resulting in confidently identified 3'UTRs for more than 78.79% of the annotated protein-coding genes in zebrafish. Most zebrafish genes undergo alternative CPA with more than a thousand genes using different dominant 3'UTRs at different stages. 3'UTRs tend to be shortest in the ovaries and longest in the brain. Isoforms with some of the shortest 3'UTRs are highly expressed in the ovary yet absent in the maternally contributed RNAs of the embryo, perhaps because their 3'UTRs are too short to accommodate a uridine-rich motif required for stability of the maternal mRNA. At two hours post-fertilization, thousands of unique poly(A) sites appear at locations lacking a typical polyadenylation signal, which suggests a wave of widespread cytoplasmic polyadenylation of mRNA degradation intermediates. Our insights into the identities, formation, and evolution of zebrafish 3'UTRs provide a resource for studying gene regulation during vertebrate development.

overall_design: 3P-Seq was used to map the 3' ends of protein-coding genes in the zebrafish genome

first: Alena

last: Shkumatava

first: Calvin

last: Jan

last: Subtelny

first: David

last: Koppstein

first: George

last: Bell

first: Hazel

last: Sive

last: Bartel


title: Kc WT Repliseq

status: Public on Jun 14 2012

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

summary:
modENCODE_submission_3630
This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The relative time of replication for all unique sequences in the Drosophila genome was determined by sequencing replication intermediates that were differentially labeled with BrdU during S-phase progression.  Briefly, cells were pulse labeled with BrdU and sorted into early, middle and late S-phase fractions.  BrdU labeled sequences from each fraction of S-phase were enriched by immunoprecipitation and sequenced on the Illumina platform.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Genotype: se/e; Sex: Female;  EXPERIMENTAL FACTORS:

last: MacAlpine

first: Yoav

last: Lubelsky

first: Joseph

last: Prinz


title: Relocalization of retinoic acid receptors from non-canonical to canonical spaced binding elements during embryoid body differentiation

city: Illkirch

first: Tao

last: YE

address: 1 rue Laurent Fries

institute: IGBMC (CNRS/INSERM/UDS)

summary: Retinoic Acid Receptors (RARs) bind RA-response elements in regulatory regions of their target genes. While canonical RAREs comprise direct repeats of the consensus 5’-RGKTCA-3’ sequence separated by 1, 2 or 5 nucleotides (DR1, DR2, DR5), we show that shortly after RA treatement of mouse embryoid bodies or F9 cells, RARs occupy a large repertoire of DR0, DR2, DR5, DR8 and IR0 elements. In vitro, RAR-RXR bind these non-canonical spacings with comparable affinities to DR2 and DR5. Most DR8 elements comprise three half sites with DR2 and DR0 spacings. This specific half site organisation constitutes a previously unrecognised, but frequent signature of RAR binding elements and acts as an RARE. At later stages of embryoid body differentiation, RARs relocalise to a restricted repertoire of sites comprising predominantly DR5 elements. Differentiation thus involves genomic relocalisation of RARs, and a switch from DR0 and DR8 at early times to DR5 at later stages.

overall_design: Examination of genomic localisation of RAR in differentiating embryoid bodies.

first: Emmanuel

last: Moutier

last: Ye

first: Mohamed-Amin

last: Choukrallah

first: Sylvia

last: Urban

first: Judit

last: Osz

first: Amandine

last: Chatagnon

first: Laurence

last: Delacroix

first: Diana

last: Langer

first: Natacha

last: Rochel

first: Dino

last: Moras

first: Gerard

last: Benoit

first: Irwin

last: Davidson


title: Nucleosome occupancy dynamics in yeast BY4741 responding to 0.4mM H2O2 over time (0-60 min)

city: Madison

first: Dana

last: Huebert

state: WI

address: 425G Henry Mall

institute: University of Wisconsin-Madison

summary: Numerous factors have been implicated in regulating gene expression changes, including changes to nucleosome occupancy.  Here we followed dynamic changes to nucleosome occupancy, gene expression and DNA binding of the transcription factor Msn2p genome-wide in yeast cells responding to hydrogen peroxide to reveal new relationships between regulators of stress-dependent gene expression.

overall_design: Nucleosome occupancy was measured by MNase-Seq in response to .4mM H2O2 in the S288c yeast derivative BY4741.  A single replicate was performed for the time-course experiment with time points at 0, 4, 12, 20, 40 and 60 minutes after treatment.

first: Audrey

last: Gasch


title: The B cell identity factor Pax5 regulates distinct transcriptional programs in early and late B lymphopoiesis

city: Vienna

first: Meinrad

last: Busslinger

address: Dr. Bohrgasse 7

institute: Instutute of Molecular Pathology

summary: Pax5 controls the identity and development of B cells by repressing lineage-inappropriate genes and activating B-cell-specific genes. Here, we used genome-wide approaches to identify Pax5 target genes in pro-B and mature B cells. In these cell types, Pax5 bound to 40% of the cis- regulatory elements defined by mapping Dnase I hypersensitive (DHS) sites, transcription start sites and histone modifications. Although Pax5 bound to 8,000 target genes, it regulated only 4% of them in pro-B and mature B cells by inducing enhancers at activated genes and eliminating DHS sites at repressed genes. Pax5-regulated genes in pro-B cells account for 23% of all expression changes occurring between common lymphoid progenitors and committed pro-B cells, which identifies Pax5 as an important regulator of this developmental transition. Regulated Pax5 target genes minimally overlap in pro-B and mature B cells, which reflects massive expression changes between these cell types. Hence, Pax5 controls B cell identity and function by regulating distinct target genes in early and late B lymphopoiesis.

overall_design: 44 samples (16 RNA-seq, 15 ChIP-seq,  6 DHS-seq, 5 Bio-ChIP-seq, 2 CAGE-seq). All but four samples in in 2 biological replicates (8819, 8275, 8095, 8666). WT and experimental samples are provided.

first: Roger

last: Revilla-i-Domingo

first: Ivan

last: Bilic

first: Bojan

last: Vilagos

first: Hiromi

last: Tagoh

first: Anja

last: Ebert

first: Ido

last: Tamir

first: Leonie

last: Smeenk

first: Andreas

last: Sommer

first: Markus

last: Jaritz

first: Johanna

last: Trupke


title: Response of Bacillus halodurans C-125 wild-type and OLE-OAP knockout cells to acute ethanol stress

city: New Haven

first: Jason

last: Wallace

state: CT

address: Biology - KBT

department: Molecular, Cellular, and Developmental Biology

institute: Yale University

summary: OLE RNA (Ornate, Large, Extremophilic RNA) is a large, noncoding RNA from extremophilic and/or anaerobic Firmicutes that binds to an integral membrane protein (OAP, OLE-Associated Protein) and localizes to the cell membrane. It is highly abundant in cells, and knockouts show increased sensitivity to short-chain alcohols, especially ethanol. We treated Bacillus halodurans C-125 cells (both wild-type and OLE-OAP knockouts) with 5% (v/v) ethanol for 3 hours to determine differences in their response to this stress. There are almost no significant differences between cells before ethanol stress, while after ethanol stress a small number (~40) genes show differences in expression between the two strains. These genes show little connection between their function, however, leading us to conclude that the majority of differential adaptation in kncokouts may occur at an earlier time or at the post-trancriptional level. These data also serve as a reference for a Gram-positive alkaliphile's response to acute ethanol stress.

overall_design: Examination of wild-type and OLE-OAP knockout cells before and after ethanol stress, in duplicate (8 samples total)

middle: G

first: Ronald

last: Breaker


title: Genistein and bisphenol A exposure cause estrogen receptor 1 to bind thousands of binding sites in a cell type-specific manner

status: Public on Jun 13 2012

city: Huntsville

last: Gertz

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute

summary: To obtain an integrated view of gene regulation in response to environmental and endogenous estrogens on a genome-wide scale, we performed ChIP-seq, to identify estrogen receptor 1 (ER) binding sites, and RNA-seq in endometrial cancer cells exposed to bisphenol A (BPA; found in plastics), genistein (GEN; found in soybean), or 17β-estradiol (E2; an endogenous estrogen).  GEN and BPA treatment induces thousands of ER binding sites and >50 gene expression changes, representing a subset of E2‑induced gene regulation changes.  Genes affected by E2 were highly enriched for ribosome-associated proteins; however, GEN and BPA failed to regulate most ribosome-associated proteins and instead enriched for transporters of carboxylic acids.  Treatment-dependent changes in gene expression were associated with treatment-dependent ER binding sites, with the exception that many genes up-regulated by E2 harbored a BPA-induced ER binding site, but failed to show any expression change after BPA treatment.   GEN and BPA exhibited a similar relationship to E2 in the breast cancer line T-47D, where cell type specificity played a much larger role than treatment specificity.  Overall, both environmental estrogens clearly regulate gene expression through ER on a genome-wide scale, although with lower potency resulting in less ER binding sites and less gene expression changes compared to the endogenous estrogen, E2.

overall_design: RNA-seq of human cancer cell lines treated with estradiol, bisphenol A, genistein or DMSO (control)

first: Richard

last: Myers


title: Small-RNAs in L4 and young adult stages

first: Jin-Wu

last: Nam

address: Nine Cambridge Center

institute: Whitehead Institute

summary: Small endogenous C. elegans RNAs from L4 and young adult worms were prepared for sequencing using a protocol derived from Batista et al., (2008) and Lau et al. (2001). The small-RNA libraries were constructed using a method that does not require a 5’ monophosphate (called 5’ monophosphate-independent method, Ambros et al., 2003) to profile secondary siRNAs that have 5’ triphosphorylated G. All preprocessed small-RNA reads were mapped to genome (ce6), allowing no mismatches. After excluding miRNAs, 21U RNAs, rRNAs, and other structural ncRNAs, the remaining reads were classified as 22G RNAs, 26G RNAs, and other siRNAs, based on their length and 5′ terminal nucleotide.

overall_design: Small-RNA libraries were sequenced in L4 and young adult stages in C.elegans.

first: Wendy

last: Johnston

first: David

last: Bartel


title: CpG islands and GC content dictate nucleosome depletion in a transcription independent manner at mammalian promoters (Phenantroline)

status: Public on Jun 12 2012

city: Marseille

first: Romain

last: Fenouil

address: Parc Scientifique et Technologique de Luminy - Case 906

department: CIML

institute: CNRS

summary: One clear hallmark of mammalian promoters is the presence of CpG islands (CGIs) at more than two thirds of genes whereas TATA boxes are only present at a minority of promoters. Using genome-wide approaches, we show that GC content and CGIs are major promoter elements in mammalian cells, able to govern open chromatin conformation and support paused transcription. First, we define three classes of promoters with distinct transcriptional directionality and pausing properties which correlate with their GC content. We further analyze the direct influence of GC content on nucleosome positioning and depletion, and show that CGIs correlate with nucleosome depletion both in vivo and in vitro. We also show that transcription is not essential for nucleosome exclusion but influences both a weak +1 and a well-positioned nucleosome at CGI borders. Altogether our data support the idea that CGIs have become an essential feature of promoter structure defining novel regulatory properties in mammals.

overall_design:
Nucleosome density and positioning were studied by high-throughput sequencing of DNA previously treated with Mnase. In parallel, ChIP-seq for PolII and H3K27ac were performed in mouse and human with different conditions to assess a potential effect of transcription on nucleosomes properties.
To exclude a possible MNase digestion bias or sequencing artefact within CGIs, we performed additional controls such as nucleosome mapping using an alternative method based on DNA digestion by a chemical agent (phenanthroline) in human Raji B-cells.

first: Pierre

last: Cauchy

first: Frederic

last: Koch

first: Nicolas

last: Descostes

first: Joaquin

middle: Z

last: Cabeza

first: Charlène

last: Innocenti

last: Ferrier

first: Salvatore

last: Spicuglia

first: Marta

last: Gut

first: Ivo

first: Jean-Christophe

last: Andrau


title: CpG islands and GC content dictate nucleosome depletion in a transcription independent manner at mammalian promoters (MNase-seq)

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Nucleosome density and positioning were studied by high-throughput sequencing of DNA previously treated with Mnase. In parallel, chIPseq for PolII and H3K27ac were performed in mouse and human with different conditions to assess a potential effect of transcription on nucleosomes properties.


title: Dynamic changes to nucleosome occupancy and genomic expression in yeast responding to oxidative stress

first: Dana

middle: J

last: Huebert

type: Genome binding/occupancy profiling by genome tiling array

type: Expression profiling by genome tiling array

platform_organism:
Saccharomyces cerevisiae
Saccharomyces cerevisiae S288C

first: Audrey

last: Gasch


title: CpG islands and GC content dictate nucleosome depletion in a transcription independent manner at mammalian promoters


title: CpG islands and GC content dictate nucleosome depletion in a transcription independent manner at mammalian promoters (ChIP-seq)


title: Wide-scale analysis of alternative polyadenylation (APA) associated with proliferation and transformation using 3'-Seq

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

country: Israel

institute: Tel Aviv University

summary: We mapped and quantified poly(A) sites in BJ and MCF10A cells under proliferative, arrested and transformed states

overall_design: Two human cell lines (BJ and MCF10A) examined under proliferative, arrested and transformed states

first: Rani

first: Reuven

last: Agami


title: ChIP-sequencing (ChIP-seq) experiments on female ESCs expressing V5-tagged REX1 and control wild-type Embryonic stem cells (ESCs)

city: Rotterdam

first: Eskeatnaf

last: Mulugeta Achame

state: Rotterdam

address: Dr Molewaterplein 50

department: Reproduction and Development

institute: Erasmusmc

summary: Evolution of the mammalian sex chromosomes has resulted in a heterologous X and Y pair, where the Y chromosome has lost most of its genes. Hence, there is a need for X-linked gene dosage compensation between XY males and XX females. In placental mammals, this is achieved by random inactivation of one X chromosome (XCI) in all female somatic cells. Up-regulation of Xist transcription on the future inactive X chromosome (Xi) acts against Tsix antisense transcription, and spreading of Xist RNA in cis triggers epigenetic changes leading to XCI. Previously, we have shown that the X-encoded E3 ubiquitin ligase RNF12 is up-regulated in differentiating mouse embryonic stem cells (ESCs)  and activates Xist transcription and XCI. Here, we have identified the pluripotency factor REX1 as a key target of RNF12 in the XCI mechanism. RNF12 causes ubiquitination and proteasomal degradation of REX1, and Rnf12 knockout mouse ESCs show an increased level of REX1. Using ChIP-seq, REX1 binding sites were detected in Xist and Tsix regulatory regions. Over-expression of REX1 in female ESCs was found to inhibit Xist transcription and XCI, whereas male Rex1+/- ESCs showed ectopic XCI. From this, we propose that RNF12 causes REX1 breakdown through dose-dependent catalysis, thereby representing an important pathway to initiate XCI. Rex1 and Xist are present only in placental mammals, which points to co-evolution of these two genes and XCI.

overall_design: 2 (one control one pulldown) samples

first: Joost

last: Gribnau

first: Cristina

last: Gontan

last: Achame

first: Wilfred

last: van IJcken

first: J

middle: A

last: Grootegoed


title: Characterization of small RNA-generating regions targeted by RNA polymerase V in Arabidopsis

status: Public on Jun 11 2012

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

summary: In plants, heterochromatin is maintained by a small RNA-based gene silencing mechanism known as RNA-directed DNA methylation (RdDM). RdDM requires the non-redundant functions of two plant-specific DNA-dependent RNA polymerases (Pol) Pol IV and Pol V.  Pol IV plays a major role in siRNA biogenesis, while Pol V may recruit DNA methylation machinery to target endogenous loci for silencing. Although small RNA-generating regions which are dependent on both Pol IV and Pol V have been identified previously, the genomic loci targeted Pol V for siRNA accumulation and silencing have not been described extensively. To characterize the Pol V-dependent, heterochromatic siRNA-generating regions in the Arabidopsis genome, we deeply sequenced the small RNA populations of wild-type and Pol V mutant plants. Furthermore, we characterized the siRNA-generating regions which were dependent on RdDM effectors and examined their dependency on Pol V.  Small RNA libraries were generated and deeply sequenced from mutant alleles dms4-1, drd1-1, dms3-1, and rdm1-4, along with their control library (“Wt(T+S)”) which has been described previously (Kanno et al. 2004 Current Biology). More than 2,000 small RNA-generating loci were identified which were greatly suppressed in Pol V mutants.

overall_design:
The Pol V-dependent, heterochromatic siRNA-generating regions were characterized in the Arabidopsis genome by deep sequencing the small RNA populations of wild-type and  Pol V mutant plants.
Deep SBS sequencing was used for small RNA profiling of immature inflorescence tissues from RNA polymerase V and RdDM mutants.

first: Tzuu-fen

last: Lee


title: The DNA methylomes of a newborn and a centenarian

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

institute: IDIBELL

type: Methylation profiling by high throughput sequencing

summary: We have developed Whole Genome Bisulfite Sequencing (WGBS) of a newborn and a centenarian to address the epigenetic drifts in human aging, which might be an alternative pathway to explain the age-associated alterations. In addition, we have analyzed the methylome of a middle-age donor (26 years).

overall_design: Examination of two DNA methylomes at the most extreme points of their lives to see differences that might contribute to explain the aged phenotype. The methylome of a middle-age donor (26 years) was also analyzed.

first: Heyn

last: Holger

first: Esteller

last: Manel


title: Comparing two transcriptome technologies - sequencing match microarrays

status: Public on Jun 10 2012

city: Cadorago

first: Martin

middle: Bastian

last: Pedersen

state: CO

address: Via Manzoni 29

department: R&D

country: Italy

institute: Sacco Srl

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

overall_design: Refer to individual Series


title: CpG islands and GC content dictate nucleosome depletion in a transcription independent manner at mammalian promoters (RNA-seq)

first: Romain

last: Fenouil

overall_design:
Nucleosome density and positioning were studied by high-throughput sequencing of DNA previously treated with Mnase. In parallel, chIPseq for PolII and H3K27ac were performed in mouse and human with different conditions to assess a potential effect of transcription on nucleosomes properties.
To investigate transcription at promoters, we analyzed together with genome-wide Pol II accumulation by ChIP-Seq, paused bidirectional transcripts associated with transcription start sites (TSS RNAs).

first: Pierre

last: Cauchy

first: Frederic

last: Koch

first: Nicolas

last: Descostes

first: Joaquin

last: Cabeza

first: Charlène

last: Innocenti

last: Ferrier

first: Salvatore

last: Spicuglia

first: Marta

last: Gut

first: Ivo

first: Jean-Christophe

last: Andrau


title: Sex-dependent RNA expression in opossum brain and liver.

city: Bethesda

first: Pavel

last: Khil

state: MD

address: 5 Memorial Dr.

institute: NIDDK

summary: To compensate for the increased dosage of X chromosomes in females one of the two X chromosomes is inactivated in eutherian mammals in an Xist-dependent manner. Xist is, however, not found in metatherians. Here we describe long non-coding RNA Rsx (RNA-on-the-silent X) that exhibits properties consistent with a role in X-inactivation in opossum. Rsx is abundantly expressed in females but not males and is transcribed from, and coats, the inactive X chromosome copy. Furthermore, when both X chromosomes are active, Rsx is silenced. We used RNA-Seq to determine exon-intron structure and expression level of Rsx in males and females.

overall_design: RNA sequencing was used to detect and characterize transcripts with strongly biased female expression.

first: Jennifer

last: Grant

first: Shantha

middle: K

last: Mahadevaiah

first: Mahesh

last: Sangrithi

first: Janine

last: Duckworth

first: John

middle: R

last: McCarrey

middle: L

last: VandeBerg

first: Marilyn

last: Renfree

first: Willie

last: Taylor

first: Greg

last: Elgar

first: Rafael

middle: D

last: Camerini-Otero

first: Michael

last: Gilchrist

first: James

last: Turner


title: PolII Cl8 ChIP-Seq experiment

status: Public on Jun 07 2012

first: DCC

last: modENCODE

summary:
modENCODE_submission_4352
This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We will precisely identify sequence elements that direct DNA replication by using chromatin immunoprecipitation of known replication initiation complexes.  These experiments will be conducted in multiple cell types and developmental tissues.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Cell Line: CME-W1-Cl.8+; Tissue: dorsal mesothoracic disc; Developmental Stage: third instar larval stage; Sex: Male;  EXPERIMENTAL FACTORS: Antibody Anti-RNA polymerase II clone CTD4H8 (target is RNA polymerase II)

first: David

last: MacAlpine

first: Heather

first: Joseph

last: Prinz


title: Genome wide identification of p63 binding sites in human neonatal foreskin keratinocytes

status: Public on Jun 08 2012

city: Belfast

first: Simon

middle: S

last: McDade

address: 97 Lisburn Road

department: CCRCB

institute: Queen's University Belfast

summary: We report here genome wide identification of p63 binding sites in cycling neonatal foreskin keratinocytes using high throughput sequencing of ChIP enriched DNA.  Analysis of gene ontology, database mining with integration with publicly available data, reveals a role for p63 in transcriptional regulation of multiple genes genetically linked to cleft palate. In addition, we identify AP-2Î±, a transcription factor which, when mutated, also results in craniofacial clefting syndrome, as a co-regulator of p63 responsive genes.

overall_design: Examination of p63 binding sites in neonatal foreskin keratinocytes

first: Dennis

last: McCance


title: Deep Sequence Analysis of non-small cell lung cancer: Integrated analysis of gene expression, alternative splicing, and single nucleotide variations in lung adenocarcinomas with and without oncogenic KRAS mutations

city: Rochester

first: Krishna

last: Kalari

state: MN

address: 200 1st ST SW

department: Department of Biomedical Statistics and Informatics

institute: Mayo Clinic

summary: In this manuscript, we have used RNA-Sequencing experiment to obtain and integrate a variety of genomic features in order to identify signaling pathways that are associated to mutant KRAS lung tumors.

overall_design: 8 lung adenocarcinomas with mutant KRAS in lung tumors and 8 lung adenocarcarcinomas without KRAS mutation of which one sample is ran twice for QC purposes.

last: Rossell

first: Brian

last: Necela

first: Yan

middle: W

last: Asmann

first: Asha

last: Nair

first: Saurabh

last: Baheti

first: Jennifer

last: Kachergus

first: Curtis

last: Younkin

first: Tiffany

last: Baker

last: Carr

first: Xiaojia

last: Tang

first: Micheal

middle: P

last: Walsh

first: High-Seng

last: Chai

first: Zhifu

last: Sun

first: Steven

last: Hart

first: Alexey

last: Leontovich

first: Asif

last: Hossain

first: Jean-Pierre

last: Kocher

first: Edith

last: Perez

last: Reisman

first: Alan

last: Fields

first: E

last: Thompson


title: non-coding RNA sequencing of upland cotton fiber and ovule

status: Public on Jun 06 2012

city: Beijing

first: Yu-Xian

last: Zhu

address: 5# Summer Palace Road

institute: College of life sciences, Peking University

summary: Three samples of cotton fiber harvested 3, 7 and 15 days post anthesis (DPA) and a sample of cotton ovule harvestd 0 DPA were used for non-coding RNA extraction and seloxa sequencing experiments, respectively.Cotton plants (Gossypium hirsutum cv. Xuzhou 142) were grown in a soil mixture in fully automated walk-in growth rooms with 300 µmol m–2 s–1 average light intensity, 60% relative humidity and temperatures set to 30C during the light period and 28C during the dark (12-h light/dark cycle). These conditions were consistent throughout the year. Small RNA molecules under 30 bases were amplified and isolated from an agarose gel. The purified DNA was used directly for cluster generation and sequencing analysis using the Illumina Genome Analyzer IIx according to the manufacturer's instructions. The 38nt sequence tags from sequencing went through data cleaning first, which included getting rid of the low-quality tags and clipping adapter sequences.

first: Qin

last: Li

first: Xiang

last: Jin

first: Guang-hui

last: Xiao

first: Yu-xian


title: Genome-wide profiling of target genes for the systemic lupus erythematosus-associated transcription factors IRF5 and STAT4

city: Uppsala

first: Chuan

last: Wang

address: The University Hospital, Entrance 70, 3rd Floor, Research Department II

department: Medical Sciences

institute: Uppsala University

summary: IRF5 and STAT4 are strongly associated with human systemic lupus erythematosus (SLE). By performing chromatin immunoprecipitation-sequencing (ChIP-Seq) in human peripheral blood mononuclear cells (PBMCs), we identified more than 7000 target genes for IRF5 and STAT4 in stimulated PBMCs. Contrarily, without stimulation IRF5 seemed to be inactive, and STAT4 only showed low levels of transcriptional regulatory activity.

overall_design: Target genes of IRF5 and STAT4 were identified in human PBMCs with or without stimulation using ChIP-Seq.

first: Johanna

last: Sandling

first: Niklas

last: Hagberg

first: Olof

last: Berggren

first: Snaevar

last: Sigurdsson

last: Karlberg

first: Lars

last: Rönnblom

first: Maija-Leena

last: Eloranta

first: Ann-Christine

last: Syvänen


title: Histone Modifications by ChIP-seq from ENCODE/University of Washington

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Richard Sandstrom mailto:sull@u.washington.edu). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu).

This track was produced as part of the ENCODE Project. This track displays genome-wide maps of histone modifications in different cell lines (http://hgwdev.cse.ucsc.edu/cgi-bin/hgEncodeVocab?type=cellType) using ChIP-seq high-throughput sequencing.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design:
Cells were grown according to the approved ENCODE cell culture protocols (http://hgwdev.cse.ucsc.edu/ENCODE/protocols/cell). Cells were cross-linked with 1% formaldehyde, and the reaction was quenched by the addition of glycine. Fixed cells were rinsed with PBS, lysed in nuclei lysis buffer, and the chromatin was sheared to 200-500 bp fragments using a Fisher Dismembrator (model 500). Sheared chromatin fragments were immunoprecipitated with specific polyclonal antibodies at 4 °C with gentle rotation. Antibody-chromatin complexes were washed and eluted. The cross-linking in the immunoprecipitated DNA was reversed and treated with RNase-A. Following proteinase K treatment, the DNA fragments were purified by phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation. A quantity of 20-50 ng of ChIP DNA was end-repaired, followed by the addition of adenine, ligation to Illumina adapters, and creation of a Solexa library for sequencing.
ChIP-seq affinity was directly measured through the raw tag density (Raw Signal), which is shown in the track as density of tags mapping within a 150 bp sliding window (at a 20 bp step across the genome). ChIP-seq affinity zones (HotSpots) were identified using the HotSpot algorithm described in Sabo et al. (2004). One percent false discovery rate thresholds (FDR 1.0%) were computed for each cell type by applying the HotSpot algorithm to an equivalent number of random uniquely mapping 36-mers. ChIP-Seq affinities (Peaks) were identified as signal peaks within FDR 1.0% hypersensitive zones using a peak-finding algorithm.
All tracks have a False Discovery Rate of 1% (FDR 1.0%).
Data were verified by sequencing biological replicates displaying a correlation coefficient > 0.9.

first: Richard

last: Sandstrom


title: The Folliculin-Fnip1 pathway deleted in human Birt-Hogg-Dube syndrome is required for B cell development.

city: bethesda

first: Seolkyoung

last: Jung

address: 10 Center Dr

department: NIAMS

institute: NIH

summary: Birt-Hogg-Dube (BHD) syndrome is an autosomal dominant disorder characterized by hamartomas of skin follicles, cystic lung disease, and renal neoplasia.  Affected individuals carry heterozygous mutations in Folliculin (FLCN), a tumor suppressor gene that becomes biallelically inactivated in kidney tumors by second-hit mutations. Similar to other factors implicated in kidney malignancies, Folliculin has been shown to modulate activation of mammalian target of rapamycin (mTOR). However, its precise in vivo function is largely unknown because germline deletion of Flcn results in early embryonic lethality in animal models. We here describe mice deficient in the newly characterized Folliculin-Interacting Protein 1 (Fnip1). In contrast to Flcn, Fnip1-/- mice develop normally, are not susceptible to kidney neoplasia, but display a striking pro-B cell block that is independent of mTOR activity. We show that this developmental arrest results at least in part from impaired V(D)J recombination and caspase-induced cell death, and that pre-recombined V(D)J and Bcl2 transgenes reconstitute pre-B and mature B cell populations respectively. We also demonstrate that conditional deletion of Flcn recapitulates the pro-B cell arrest of Fnip1-/- mice. Our studies thus demonstrate that the Flcn-Fnip complex deregulated in BHD syndrome is absolutely required for B cell differentiation and that it functions both through mTOR dependent and independent pathways.

overall_design: RNASeq data for two pro-B cell subsets (fraction B and CC') isolated from wt and Fnip1-/- mice

first: Masaya

last: Baba

first: Jonathan

last: Keller

first: Hong-Wei

last: Sun

first: Wolfgang

last: Resch

first: Stefan

last: Kuchen

first: Huang-Chang

last: Suh

first: Hisashi

last: Hasumi

first: Yukiko

first: Kyong-Rim

last: Kieffer-Kwon

first: Carme

last: Gallego Gonzalez

first: Robert

last: Hughes

first: Mara

middle: E

last: Klein

first: Paul

last: Bible

first: Laura

last: Schmidt

first: Marston

last: Linehan

first: Rafael

last: Casellas


title: The Stat3/GR interaction code: predictive value of direct/indirect DNA recruitment for transcription outcome

city: MONTREAL

first: David

last: Langlais

state: QC

address: 740 Ave Dr Penfield, rm 4203, McGill Genome Centre

department: Human Genetics

institute: McGill University

summary: Transcription factor recruitment to genomic sites of action is primarily due to direct protein:DNA interactions. The subsequent recruitment of co-regulatory complexes leads to either transcriptional activation or repression. In contrast to this canonical scheme, some transcription factors such as the glucocorticoid receptor (GR) behave as transcriptional repressors when recruited to target genes through protein tethering. We have investigated the genome-wide prevalence of tethering between GR and Stat3 and found non-reciprocal interactions, namely that GR tethering to DNA-bound Stat3 results in transcriptional repression whereas Stat3 tethering to GR results in synergism. Further, other schemes of GR and Stat3 co-recruitment to regulatory modules result in transcriptional synergism, including neighbouring and composite binding sites. The results indicate extensive transcriptional interactions between Stat3 and GR; further, they provide a genome-wide assessment of transcriptional regulation by tethering and a molecular basis for integration of signals mediated by GR and Stats in health and disease.

overall_design: ChIP-seq analysis of Stat3 and GR binding sites in pituitary corticotroph AtT-20 cell model. Five independant ChIPs were pooled prior library preparation for each contitions: STAT3 (LIF), STAT3 (Dex+LIF), GR (Dex+LIF), GR (Dex) and control IgG.

first: Catherine

last: Couture

first: Jacques

last: Drouin


title: Identification of Transcription Factor UNC-62::GFP Binding Regions in YA

status: Public on Jun 04 2012

city: Toronto

first: DCC

last: modENCODE

address: MaRS Centre, South Tower, 101 College Street, Suite 800

institute: Ontario Institute for Cancer Research

summary:
modENCODE_submission_3584
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP600(official name : OP600 genotype : unc119(ed3);wgIs600(unc-62::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The UNC-62::EGFP fusion protein is expressed in the correct unc-62 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the UNC-62 transcription factor. made_by : S Kim ); Developmental Stage: Day Four Young Adult; Genotype: unc119(ed3);wgIs600(unc-62::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage Day Four Young Adult; Target gene unc-62; Strain OP600(official name : OP600 genotype : unc119(ed3);wgIs600(unc-62::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The UNC-62::EGFP fusion protein is expressed in the correct unc-62 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the UNC-62 transcription factor. made_by : S Kim ); temp (temperature) 20 degree celsius

first: Mei

last: Zhong

first: Mike

last: Snyder

first: Cindie

last: Slightam

first: Stuart

last: Kim

first: John

last: Murray

last: Waterston

first: Mark

last: Gerstein

first: Wei

last: Niu

first: Judi

last: Janette

first: Debasish

last: Raha

first: Ashish

last: Agarwal

first: Valerie

last: Reinke

first: Mihail

last: Sarov

first: Anthony

last: Hyman


title: RIP-seq from ENCODE/SUNY Albany

first: ENCODE

last: DCC

summary:
This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Scott Tenenbaum mailto:STenenbaum@uamail.albany.edu). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu).

The RNA binding protein (RBP) associated mRNA sequencing track (RIP-Seq) is produced as part of the Encyclopedia of DNA Elements (ENCODE) Project (http://hgwdev.cse.ucsc.edu/ENCODE/index.html). This track displays transcriptional fragments associated with RBP in cell lines (http://hgwdev.cse.ucsc.edu/cgi-bin/hgEncodeVocab?type=cellType) K562 and GM12878, using Ribonomic profiling via Illumina SBS.
In eukaryotic organisms gene regulatory networks require an additional level of coordination that links transcriptional and post-transcriptional processes. Messenger RNAs have traditionally been viewed as passive molecules in the pathway from transcription to translation. However, it is now clear that RNA-binding proteins play a major role in regulating multiple mRNAs in order to facilitate gene expression patterns. These tracks show the associated mRNAs that co-precipitate with the targeted RNA-binding proteins using RIP-Seq profiling.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design:
RBP-mRNA complexes were purified from cells grown according to the approved ENCODE cell culture protocols (http://hgwdev.cse.ucsc.edu/ENCODE/protocols/cell). RNA samples were amplified and converted to cDNA with the Nugen (http://www.nugeninc.com/) Ovation© RNA-Seq System and prepped for sequencing with the Illumina (http://www.illumina.com/) mRNA-Seq protocol. Approximately 30 million single end sequencing reads were obtained for each K562 and GM12878. RIP samples were analyzed for signal that was at or above the 60th percentile and statistically enriched compared to the negative control. Sequences were analyzed using TopHat (http://tophat.cbcb.umd.edu/) (Trapnell et al., 2009) with Bowtie (http://bowtie-bio.sourceforge.net/index.shtml) (Langmead et al., 2009).
Peaks were called from the top 40% of TopHat normalized reads, with a max gap, min run of (24:48). Unions of overlapping peak regions from total RNA replicates (RIP-Input) are presented with p-value from a one tailed t-test for average signal from replicates versus 0 (no cut-off was used for totals). Replicate overlap for positive RIP treatment peaks (ELAVL1 and PABPC1) are presented with a p-value from one tailed t-test versus signal for same the region in negative control replicates (T7-tag). RIP peaks were from sequences longer than 120 bp and p-value < .05. For both totals (RIP-input) and RIPs, the peak scores are scaled relative p-values between treatment and control.

first: Scott

last: Tenenbaum