title: seq-WA30534819_H3K4me3_N2_MXemb

city: Chapel Hill

first: Everett

last: Zhou

state: NC

address: 1000 Manning Dr.

institute: UNC

summary:
modENCODE_submission_3169
We analyzed H3 lysine 4 trimethylation levels in the C. elegans genome using chromatin immunoprecipitation followed by Illumina sequencing. We used wild type (N2) mixed developmental stage embryos and performed the experiment in two biological replicates.

overall_design:
This series consists of two biological replicates of H3K4me3 ChIP-seq experiments and their input sequences.

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

first: Sevinc

last: Ercan

first: Kohta

last: Ikegami

first: Jason

last: Lieb


title: Hoxc9 ChIP-seq in differentiating motor neurons

status: Public on Sep 08 2010

city: University Park

first: Shaun

last: Mahony

state: PA

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

country: USA

institute: Penn State University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The expression of v5-tagged Hoxc9 is induced and ChIP-seq is used to profile genome-wide occupancy in differentiating motor neurons

overall_design: The differentiation of ventral motor neurons is induced by treating embryonic stem cell cultures with retinoic acid and hedgehog signaling. Here, ChIP-seq is used to profile the genome-wide occupancy of Hoxc9 after five days of differentiation.

first: Heekyung

last: Jung

first: Julie

last: Lacombe

first: Esteban

middle: O

last: Mazzoni

first: Karel

middle: F

last: Liem

first: Jonathan

last: Grinstein

first: Debnath

last: Mukhopadhyay

first: David

middle: K

last: Gifford

first: Richard

middle: A

last: Young

first: Kathryn

middle: V

last: Anderson

first: Hynek

last: Wichterle

first: Jeremy

middle: S

last: Dasen


title: Genome-wide mapping of RNA Pol-II promoter usage in mouse tissues by ChIP-seq

status: Public on Sep 07 2010

city: Philadelphia

first: Ravi

last: Gupta

address: 3601 Spruce Street

department: Center for Systems and Computational Biology, Molecular and Cellular Oncogenesis Program

institute: The Wistar Institute

summary: We report active promoters in five adult mouse tissues - brain, kidney, liver, lung and spleen using ChIP-Seq aganist RNAP-II antibody. We identified 38,639 active RNAP-II transcribed promoters, including 12,270 novel promoters. Of these, 6384 promoters are tissue specific which are CpG poor and contain multiple core promoter elements. By identifying the RNAP-II bound promoter(s) we found that 37% of the protein coding genes use alternative promoters in the five mouse tissues. Roughly 34% of the novel promoters are loacted in CpG-islands suggesting that novel promoters are mostly tissue specific.

overall_design: Study of active promoters in five adult mouse tissues

first: Hao

last: Sun

first: Jiejun

last: Wu

first: Priyankara

last: Wickramasinghe

first: Sharmistha

last: Pal

first: Anirban

last: Bhattachrayya

first: Francisco

middle: J

last: Agosto-Perez

first: Louise

middle: C

last: Showe

first: Tim

middle: H

last: Huang

first: Ramana

last: Davuluri


title: Genome-wide binding profile for Heat Shock Factor (HSF).

status: Public on Sep 02 2010

city: Farmington

first: Michael

middle: Joseph

last: Guertin

state: CT

address: 400 Farmington Ave

department: Center for Cell Analysis and Modeling

institute: University of Connecticut

summary: Sequence-specific transcription factors (TFs) are critical for specifying patterns and levels of gene expression, but the DNA elements to which they can bind are not always sufficient to specify their binding in vivo.  In eukaryotes, the binding of a TF is in competition with a constellation of other proteins, including histones which package DNA into nucleosomes.  Here, we examine using the ChIP-seq assay, the genome-wide distribution of Drosophila Heat Shock Factor (HSF), a TF whose binding activity is mediated by heat shock-induced trimerization.  We detect HSF binding to 464 sites, the vast majority of which contain HSF Sequence-binding Elements (HSEs) in Drosophila S2 cells, but these HSF-bound sites represent only a small fraction of HSEs present in the genome.  We find a strong correlation of bound HSEs to active chromatin marks present prior to HSF binding, indicating an HSE’s residence in open chromatin is a primary determinant of whether HSF can bind following heat shock.

overall_design: A single mock immunoprecipitation (IP) using the pre-innoculated animal serum was used as a background dataset for this study.  For each condition (NHS and 20minute HS), we performed two independent HSF-ChIP-seq experiments.  In addition, we performed two independent HSF-ChIP-seq experiments for each condition (NHS and 20minute HS) in cells that were highly depleted of HSF by RNAi.

first: John

middle: T

last: Lis


title: Epigenomic profiling of hASC adipogenesis

status: Public on Sep 30 2010

city: Cambridge

first: Tarjei

last: Mikkelsen

state: MA

address: 7 Cambridge Center

institute: Broad Institute

summary: hASC pre-adipocyte cells were grown to confluence and induced to differentiate in adipogenic media.

overall_design: Examination of 6 histone modifications and CTCF at 4 time points and PPARG at 1 time point using ChIP-Seq

first: Zhao

last: Xu

first: Jeffrey

middle: M

last: Gimble

first: Eric

last: Lander

first: Evan

middle: D

last: Rosen


title: Gene expression profiling on bronchoalveolar lavage (BAL) cells treated with all-trans-retinoic acid (ATRA)

status: Public on Sep 04 2010

city: Gauting, Munich

first: Srinivas

last: Mamidi

state: Bayern

address: Robert Koch Allee 29

department: Clinical Cooperation Group Inflammatory Lung Diseases

country: Germany

institute: Helmholtz Center Munich

summary:
All-trans retinoic acid (ATRA) is a potent retinoid, which has been used successfully in different clinical settings as a potential drug to treat COPD and emphysema. In alveolar macrophages, ATRA selectively down-regulates MMP-9 and up-regulates TIMP-1 expression.
In the present study, we analyzed additional genes modulated by ATRA by performing mRNA expression array on alveolar macrophages after treatment with ATRA.

overall_design: Total RNA was isolated from BAL cells cultivated either in the presence of liposomal ATRA or left untreated for 3 days. Total RNA from five independent donors were pooled at 0.4 µg each to give a final amount of 2µg. This pooled RNA was used for microarray analysis using the Affymatrix array

first: Thomas

middle: P

last: Hofer

first: Reinhard

last: Hoffmann

first: Loems

last: Ziegler-Heitbrock

first: Marion

last: Frankenberger


title: Global Changes following N-deprivation in Chlamydomonas: Illumina sequencing

status: Public on Sep 25 2010

city: East Lansing

first: Guangxi

last: Wu

state: MI

address: S308 Plant Bio Bld

institute: Michigan State University

type: Expression profiling by high throughput sequencing

summary: Chlamydomonas reinhardtii forms lipid droplets rich in triacylglycerols when nutrient-deprived. To begin studying the mechanisms underlying this process, N-deprivation was used to induce triacylglycerol accumulation and changes in developmental programs such as gametogenesis. Comparative global analysis of transcripts under induced and non-induced conditions was applied as a first approach to study molecular changes that promote or accompany triacylglycerol accumulation in cells encountering a new nutrient environment.  Towards this goal, high-throughput sequencing technology was employed to generate large numbers of expressed sequence tags of 8 biologically independent libraries (6 Illumina libraries, 2 454 libraries), four for each condition, N-replete and N-deprived, that allowed a statistically sound comparison of expression levels under the two tested conditions. Inferences on metabolism based on transcriptional analysis can only be indirect but were supported in parts by biochemical experiments. N-deprivation led to a marked redirection of metabolism as the carbon source acetate was no longer converted to cell building blocks by the glyoxylate cycle and gluconeogensis, but funneled directly into fatty acid biosynthesis. Protein biosynthesis and photosynthesis were down-regulated and genes of gametogenesis activated.  A notable finding was that the genes encoding photosynthetic accessory PSBS proteins of currently unclear function in C. reinhardtii were strongly expressed following N-deprivation, providing a clue to their physiological role. Lipase-encoding genes were found to be some of the most regulated following N-deprivation, suggesting a remodeling of membranes under these conditions. The data provided here represent a rich source for the exploration of the mechanism of oil accumulation in microalgae.

overall_design: Examining N-replete and N-deprived conditions. Three biological replicates each condition.

first: Christoph

last: Benning


title: PHF8 mediates histone demethylation events in cell cycle progression

status: Public on Sep 01 2010

city: La Jolla

last: Rosenfeld

state: CA

address: 9500 Gilman Drive

department: School of Medicine

institute: HHMI/UCSD

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

overall_design: Refer to individual Series


title: PHF8 mediates histone demethylation events in cell cycle progression [ChIP-Seq]

summary: While reversible histone modifications are linked to an ever-expanding range of biological functions, the demethylases for histone H4 lysine 20 and their potential regulatory roles remain unknown.  Here, we report that the PHD and Jumonji C (JmjC) domain-containing protein, PHF8, while utilizing multiple substrates, including H3K9me1/2 and H3K27me2, also functions as an H4K20me1 demethylase. PHF8 is recruited to promoters by its PHD domain based on interaction with H3K4me2/3 and controls G1/S transition in conjunction with E2F1, HCF-1 and Set1A, at least in part, by removing the repressive H4K20me1 mark from a subset of E2F1-regulated gene promoters. Phosphorylation-dependent PHF8 dismissal from chromatin in prophase is apparently required for the accumulation of H4K20me1 during early mitosis, which might represent a component of the Condensin II loading process. Accordingly, the HEAT repeat clusters in two non-SMC Condensin II subunits, N-CAPD3 and N-CAPG2, are capable of recognizing H4K20me1, and ChIP-seq. analysis demonstrate a significant overlap of Condensin II and H4K20me1 sites in mitotic HeLa cells. Thus, the identification and characterization of an H4K20me1 demethylase, PHF8, has revealed an intimate link between this enzyme and two distinct events in cell cycle progression.

overall_design: unsynchronized HeLa cells were used to profile H3K4me2 and E2F1; unsynchronized or G1 or G1/S synchronized HeLa cells were used to profile PHF8; M phase synchronized HeLa cells were used to profile SMC4 and H4K20me1

first: WeWen

last: Liu

first: Bogdan

last: Tanasa

first: Oksana

last: Tyurina

first: Tian

middle: Y

last: Zhou

first: Reto

last: Gassmann

first: Wei

first: Kenneth

last: Ohgi

first: Chris

last: Benner

first: Ivan

last: Garcia-Bassets

first: Aneel

last: Aggarwal

first: Arshad

last: Desai

first: Pieter

last: Dorrestein

first: Christopher

last: Glass

middle: G


title: miRNA expression profile analysis of Clonorchis sinensis by Solexa deep sequencing

status: Public on Sep 03 2010

city: Guangzhou

first: Zhu

last: Xingquan

state: Guangdong Province

address: 483 Wushan Street, Tianhe District

department: College of Veterinary Medicine

country: China

institute: South China Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: Clonorchis sinensis is a zoonotic parasite causing clonorchiasis associated with human diseases such as biliary calculi, cholecystitis, liver cirrhosis, and is classified as carcinogenic to humans for cholangiocarcinoma. MicroRNAs (miRNAs) are non-coding, regulating small RNA molecules essential for the complex life cycle of parasites and involved in parasitic infections. To identify and characterize miRNAs expressed in adult C. sinensis residing chronically in the biliary tract, we developed an integrative approach combining deep sequencing, bioinformatic predictions with stem-loop real-time PCR analysis. Here we report the use of this approach to identify and clone 6 new and 62,512 conserved C. sinensis miRNAs which belong to 284 families. There is strong bias on families, family members and sequence nucleotides in C. sinensis. Uracil is the dominant nucleotide, particularly at positions 1, 14 and 22, which were located approximately at the beginning, middle and the end of conserved miRNAs. There is no significant “seed region” at the first and ninth positions commonly found in human, animals and plants. Categorization of conserved miRNAs indicated that miRNAs of C. sinensis are still innovated and concentrated along three branches of the phylogenetic tree leading to bilaterians, insects and coelomates. There are two miRNA strategies in C. sinensis for its parasitic life: keeping a large category of miRNA families of different animals and keeping a stringent conserved seed region with high active innovation in other place of miRNA mainly in the middle and the end, which are perfect for the parasite to perform its complex life style and for host changes. The present study represents the first large scale characterization of C. sinensis miRNAs, which have implications for understanding the complex biology of this zoonotic parasite, as well as the miRNA studies of other related species such as Opisthorchis felineus and O. viverrini of human and animal health significance.

overall_design: Analysis of miRNA profile in parasite of C. sinensis

first: Xu

last: Minjun


title: modENCODE_White Lab: genome-wide ChIP data of NW-GFP-Goat[eve] from E8-16h on Illumina Genome Analyzer.

status: Public on Sep 16 2010

city: Chicago

first: Kevin

middle: P.

last: White

state: IL

address: 900 E. 57th STR. 10th FL.

department: Institute for Genomics and Systems Biology

institute: University of Chicago

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor NW-GFP-Goat[eve] from E8-16h generated by ChIP and analyzed on Illumina Genome Analyzer.

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:
A validated dataset is comprised of three biological replicates for ChIP-chip experiments and two replicates for ChIP-seq and meet the modENCODE quality standards. The control sample is the chromatin Input used for ChIP. Most factors binding profiles are generated by using specific antibodies for the protein of interest. However, some factors have been tagged by GFP in a transgenic line. In that case, ChIP is generated using an anti-GFP antibody.

This submission represents the ChIP-seq component of the study.

first: Nicolas

last: Negre

first: Nicholas

last: Bild


title: Characterization and comparative profiling of microRNA transcriptomes in bighead carp and silver carp

city: Wuhan

last: Chi

address: 7# Donghu South road

institute: Insititute of Hydrobiology

summary: We applied high throughput sequencing technology to identify microRNA genes in bighead carp and silver carp. We identified 167 conserved miRNAs in bighead carp and 166 in silver carp. By two computational stragegies, we obtained 39 novel miRNAs in bighead carp and 54 in silver carp, for which, no homologs were found in other species.  Several miRNA* sequences were found in our dataset as well, some particular ones might have gene regulation function. Gain and loss of family members were observed in several miRNA families, which partially reflected the fate of miRNA gene duplicates.

sample_organism:
Hypophthalmichthys nobilis
Hypophthalmichthys molitrix

overall_design: Total RNA of juvenile bighead carp and silver carp were sequenced on one Solexa lane, respectively.

first: Chaobo

last: Tong

first: Xiaoni

last: Gan

first: Shunping

last: He


title: The DNA methylome of human peripheral blood mononuclear cells

city: Shenzhen

first: Hong

middle: zhi

last: Cao

state: Guangdong

address: F5, Main Building, Beishan Industrial Zone, Beishan Road, Yantian District

department: Bioinformatics

institute: BGI-SHENZHEN

type: Methylation profiling by high throughput sequencing

summary: DNA methylation plays a vital role in genome dynamics and, in the human genome, occurs predominantly at cytosine guanine dinucleotide (CpG) sites. The diploid haploid human genome analysed here contains around 2060 million CpG sites (methylome) where DNA methylation can vary, affecting many biological processes in health and disease. Using whole-genome bisulfite sequencing, we report the essentially complete (92.6282%) methylome of human peripheral blood mononuclear cells (PBMC) which constitute an important source for clinical blood tests world-wide. We find the majority of CpG sites (68.4% at false positive rate of 0.46%) and only <0.2% of non-CpG sites to be methylated, demonstrating that non-CpG cytosine methylation is negligible in human PBMC.  Analysis of the PBMC methylome revealed a rich landscape of epigenomic data for 20 distinct features including regulatory, protein-coding, RNA gene coding, non-coding and repeat sequences.  Alu element mobility, for instance, was found to negatively correlate with their methylation levels, emphasizing the critical role of DNA methylation in genome stability. Integration of our methylome data with the previously determined genome sequence of the same Asian individual analysed here, enabled a first assessment of allele-specific methylation (ASM) differences between the two haploid methylomes of any individual. Using a conservative cut-off (p <0.001), we identified 599 haploid differentially methylated regions (hDMRs) covering 287 genes. Of these, 76 genes had hDMRs within 2kb of their transcriptional start sites of which >80% displayed allele-specific expression (ASE) after random testing using TA clone sequencing of the same PBMC sample. These data show, that ASM is a recurrent phenomenon and highly correlated with ASE, suggesting that imprinting may be more common than previously thought. Our study not only provides a comprehensive resource for future epigenomic research but also demonstrates a paradigm of large-scale epigenomics studies through new sequencing technology.

overall_design: We report the essentially complete (92.6282%) methylome of human peripheral blood mononuclear cells (PBMC) which constitute an important source for clinical blood tests world-wide.

middle: Z


title: Enhanced Pathogenicity of Th17 cells Generated in the Absence of Transforming Growth Factor-β Signaling: ChIPSeq

status: Public on Aug 31 2010

city: Bethesda

first: Lai

last: Wei

state: MD

address: 10 Center Dr. Room 2B47

institute: NIH/NEI/NCCAM

summary: CD4+ T cells that selectively produce interleukin (IL)-17, are critical for host defense and autoimmunity. Crucial for T helper17 (Th17) cells in vivo, IL-23 has been thought to be incapable of driving initial differentiation. Rather, IL-6 and transforming growth factor (TGF)-β1 have been argued to be the factors responsible for initiating specification. Herein, we show that Th17 differentiation occurs in the absence of TGF-β signaling. Neither IL-6 nor IL-23 alone efficiently generated Th17 cells; however, these cytokines in combination with IL-1β effectively induced IL-17 production in naïve precursors, independently of TGF-β. Epigenetic modification of the Il17a/Il17f and Rorc promoters proceeded without TGF-β1, allowing the generation of cells that co-expressed Rorγt and T-bet. T-bet+Rorγt+ Th17 cells are generated in vivo during experimental allergic encephalomyelitis (EAE), and adoptively transferred Th17 cells generated with IL-23 in the absence of TGF-β1 were more pathogenic in this experimental disease. These data suggest a new model for Th17 differentiation. Consistent with genetic data linking the IL23R with autoimmunity, our findings re-emphasize the role of IL-23 and therefore have important implications for the development of new therapies.

overall_design: Examination of Stat3 binding and H3K4me and H3Ac in helper T cells.

first: Kamran

last: Ghoreschi

first: Arian

last: Laurence

first: Xiang-Ping

last: Yang

first: Cristina

last: Tato

first: Mandy

last: McGeachy

first: Joanne

last: Konkel

first: Haydeé

middle: L

last: Ramos

first: Todd

last: Davidson

last: Bouladoux

first: John

last: Grainger

first: Qian

last: Chen

first: Yuka

last: Kanno

first: Wendy

last: Watford

first: Hong-Wei

last: Sun

first: Gérard

last: Eberl

first: Ethan

last: Shevach

first: Yasmine

last: Belkaid

first: Daniel

last: Cua

first: Wanjun

last: O'Shea


title: Small RNA sequencing and analysis of two ants: Camponotus floridanus and Harpegnathos saltator

status: Public on Aug 27 2010

city: shenzhen

first: zhiyong

last: huang

institute: BGI-Shenzhen, Shenzhen 518083, China

summary: Deep sequencing of small RNA from two Ants: Camponotus floridanus and Harpegnathos saltator

sample_organism:
Camponotus floridanus
Harpegnathos saltator

overall_design: Analysis of small RNA expression profile from different specimens: egg,larva,male,minor and major for Camponotus floridanus while egg,larva,male,worker and gammergate for Harpegnathos saltator

first: Shelley

last: Berger

first: Danny

last: Reinberg

first: Jun

last: Wang

first: Jürgen

last: Liebig


title: PTIP promotes chromatin changes critical for immunoglobulin class switch recombination

status: Public on Aug 25 2010

city: Charlottesville

first: Chongzhi

last: Zang

state: VA

institute: University of Virginia

summary: Programmed genetic rearrangements in lymphocytes require transcription at antigen receptor genes to promote accessibility for initiating double-strand break (DSB) formation critical for DNA recombination and repair. Here we show that activated B cells deficient in the PTIP component of the MLL3 (mixed-lineage leukemia 3) /MLL4 complex display impaired histone methylation (H3K4me3) and transcription initiation of downstream switch regions at the immunoglobulin heavy-chain (Igh) locus leading to defective immunoglobulin class-switching.  We also show that PTIP accumulation at DSBs contributes to class-switch recombination (CSR) and genome stability independently from Igh switch transcription. These results demonstrate that PTIP promotes specific chromatin changes that control the accessibility of the Igh locus to CSR, and suggest a non-redundant role for the MLL3/MLL4 complex in altering antibody effector function.

overall_design: Genome-wide analysis of histone modifications, PTIP, and Pol II in PTIP-WT and PTIP-KO mouse activated B cells.

first: Jeremy

middle: A

last: Daniel

first: Margarida

last: Santos

first: Zhibin

first: Kristopher

middle: R

last: Schwab

first: Mila

last: Jankovic

first: Darius

last: Filsuf

first: Hua-Tang

first: Anna

last: Gazumyan

first: Arito

last: Yamane

first: Young-Wook

last: Cho

first: Kai

last: Ge

first: Weiqun

last: Peng

first: Michel

last: Nussenzweig

first: Rafael

last: Casellas

first: Gregory

last: Dressler

first: Keji

last: Zhao

first: André


title: ChIP-Seq sequencing of novel interactors of H3K4me3, H3K36me3 and H3K9me3

status: Public on Sep 17 2010

city: Nijmegen

first: Hendrik

last: Marks

address: Geert Grooteplein 26/28

department: Molecular Biology

country: Netherlands

institute: Radboud University Nijmegen, RIMLS

summary: This study describes the epigenetic profiling of the novel interactors of H3K4me3, H3K36me3 or H3K9me3. The interactors were ChIP-Seq profiled by their GFP tag in stably transfected HeLa (Kyoto) cells. The interactors include GATAD1, Sgf29, BAP18, TRRAP, PHF8, N-PAC and LRWD1 (including replicates), as well as an GFP ChIP-Seq profile on non-transfected HeLa cells (negative control). Also included are the profiles of the histone modifications themselves (H3K4me3, H3K27me3, H3K9me3, H3K36me3, H3K9/14Ac and H3K79me3)

overall_design: ChIP-Seq profiling of 8 proteins by their GFP tag in stably transfected cells HeLa (Kyoto) cells, 6 replicas, as well as ChIP-Seq profiling of 6 histone modifications in wt HeLa (Kyoto) cells

first: Michiel

last: Vermeulen

first: H

last: Eberl

first: Filomena

last: Matarese

first: Sergei

last: Denissov

first: Falk

last: Butter

first: Kenneth

middle: K

last: Lee

first: Jesper

middle: V

last: Olsen

first: Anthony

last: Hyman

last: Stunnenberg

first: Matthias

last: Mann


title: Global analysis of in vivo EGR1-binding sites in erythroleukemia cell K562 using chromatin immunoprecipitation and massively parallel sequencing

city: Nanjing

first: Xiaolong

last: Shi

state: Jiangsu

address: sipailou 2

department: State Key Laboratory of Bioelectronics

institute: Southeast University

summary: Early growth response gene 1 (EGR1) has been implicated in megakaryocyte differentiation induced by PMA (phorbol 12-myristate 13-acetate). The identification of direct EGR1 target genes in global scale is critical for our understanding of how EGR1 contributes to this process. In this study, we provide a global survey on the binding location of EGR1 in the K562 cell treated by PMA using chromatin immunoprecipitation and massively parallel sequencing (ChIP-Seq). K562 is a human erythroleukemia cell line, which is situated in the common progenitor stage of megakaryocytic and erythroid lineages of the hematopoietic stem cell differentiation and its normally following differentiation is blockaded. Upon exposure to PMA stimuli, K562 cell can be induced into megakaryocytic cell, which provides a model for the study of transcriptional control networks. Over 14 000 highly confident in vivo EGR1 binding sites were identified in PMA treated K562 cell. More than 70% of these genomic sites associated with EGR1 binding were located around annotated gene regions. This whole genome study on the EGR1 targets may help a better understanding of the EGR1 regulated genes and the downstream pathway in megakaryocyte differentiation.

overall_design: The in vivo binding locations of EGR1 in K562 cell treated with PMA (phorbol 12-myristate 13-acetate, 10 ng/ml for 2 hours) were identified using chromatin immunoprecipitation combing with massively parallel sequencing (ChIP-Seq) based on AB SOLiD System 2.0.

first: Chao

last: Tang

first: Zuhong

last: Lu


title: Small RNA profiling of RNase III enzyme deficient DN3 thymocytes, Tregs, activated CD4+ T cells, and embryonic fibroblasts

status: Public on Aug 18 2010

city: Fitzroy

first: Mark

last: Chong

state: Victoria

address: 9 Princes Street

country: Australia

institute: St Vincent's Institute of Medical Research

summary:
Here we analyze the small RNA species in the following:
1. DN3 thymocytes following inactivation of LoxP flanked Drosha and Dicer alleles with Lck-cre
2. Tregs following inactivation of LoxP flanked Drosha and Dicer alleles with CD4-cre
3. activated CD4+ T cells following inactivation of LoxP flanked Drosha and Dicer alleles with CD4-cre
4. MEFs following inactivation of LoxP flanked Drosha and Dicer alleles with Rosa26-CreER and 4-OH tamoxifen treatment

overall_design: Fractionation of small RNAs (19-30nt) and cloning of only RNA with 5' phosphates and 3' hydroxyls


title: Alternative expression analysis by RNA sequencing (comparison of 5-FU sensitive and resistant colorectal cancer cell lines)

city: Vancouver

first: Malachi

last: Griffith

state: BC

address: 675 West 10th Avenue

department: Genome Sciences Centre

country: Canada

institute: British Columbia Cancer Agency

summary: In Alternative Expression Analysis (ALEXA)-Seq we developed a method to analyze massively parallel RNA sequence data to catalogue transcripts and assess differential and alternative expression of known and predicted messenger RNA (mRNA) isoforms in cells and tissues. As proof-of-principle, we applied the approach to a comparison of fluorouracil responsive and non-responsive human colorectal cancer cell lines. The sensitivity and specificity of the approach were assessed by comparison to exon tiling and splicing microarrays. Validations were conducted by reverse transcription polymerase chain reaction (PCR), quantitative PCR and Sanger sequencing. We observed global disruption of splicing in resistant cells characterized by expression of novel mRNA isoforms resulting from exon skipping, alternative splice site usage and intron retention. Alternative expression annotation databases, source code, a data viewer and other resources to facilitate analysis are available at our website: www.AlexaPlatform.org.  See Griffith et al. 2010 in Nature Methods for further details.

overall_design:
Two cell lines, 'MIP101' and 'MIP/5FU' were sequenced by Illumina paired end sequencing.  A total of ~263 million paired reads were generated.  80% of these were paired 42-mer reads and the remainder were paired 36-mer reads.  See Griffith et al, 2010 in Nature Methods for further details.
SRA center name:  BCCAGSC

first: Obi

first: Jill

last: Mwenifumbo

first: Rodrigo

last: Goya

first: A

middle: S

last: Morrissy

first: Ryan

last: Morin

first: Richard

last: Corbett

first: Michelle

middle: J

first: Ying-Chen

last: Hou

first: Trevor

last: Pugh

first: Gordon

last: Robertson

first: Suganthi

last: Chittaranjan

first: Adrian

last: Ally

first: Jennifer

last: Asano

first: Susanna

last: Chan

first: Haiyan

middle: I

last: Li

first: Helen

last: McDonald

first: Kevin

last: Teague

first: Yongjun

first: Thomas

last: Zeng

first: Allen

last: Delaney

first: Martin

last: Hirst

first: Gregg

middle: B

first: Steven

last: Jones

first: Isabella

last: Tai

first: Marco

last: Marra


title: Genome-wide map of PAX3-FKHR binding sites in rhabdomyosarcoma

status: Public on Aug 17 2010

first: Sean

last: Davis

address: 37 Convent Drive, Room 6138

institute: National Cancer Institute

summary: We report the genome-wide maps of PAX3-FKHR binding sites.  Chromatin immunoprecipitation was performed against PAX3-FKHR positive (Rh4) and PAX3-FKHR negative (RD) rhabdomyosarcoma cells with a monoclonal antibody (pFM2) specific for the fusion region of PAX3-FKHR.  We obtained 4 million sequence tags for both input and ChIP DNA that aligned to the human genome.  We identified 1,463 binding sites from ChIP-seq of Rh4 cells, none of which appeared from ChIP-seq of fusion negative RD cells. The PAX3-FKHR binding sites were found to associate with 1,072 genes in RMS cells.  The data shows that PAX3-FKHR binds to the same sites as PAX3, at the enhancers for MYF5, FGFR4, and the MYOD core enhancer previously shown to be regulated by PAX3.  Moreover, our dataset has the precision for rapid identification and validation of novel and specific sequences required for the enhancer activity of MYOD and FGFR4.  The genome wide analysis reveals that the PAX3-FKHR sites are: 1) mostly distal to transcription start sites; 2) conserved; 3) enriched for PAX3 motifs; and 4) strongly associated with genes over-expressed in PAX3-FKHR positive RMS cells and tumors.  There is little evidence in our dataset for PAX3-FKHR binding at the promoters.  In one instance, we show two intronic enhancer elements for MET, rather than at the previously described promoter.  The genome-wide analysis further illustrates a strong association between PAX3 and E-box motifs in these binding sites, suggestive of a common co-regulation for many target genes.  The map of PAX3-FKHR binding sites provides new links for PAX3 and PAX3-FKHR functions and new targets for RMS therapy.

overall_design: Examination of PAX3-FKHR binding sites in translocation-positive rhabdomyosarcoma cells via ChIP-seq with an antibody specific for the fusion protein.

first: Liang

last: Cao

first: Paul

last: Meltzer

first: Sven

last: Bilke


title: High-throughput sequencing analyses of two ants: Camponotus floridanus and Harpegnathos saltator

first: zhiyong

last: huang

platform_organism:
Camponotus floridanus
Harpegnathos saltator


title: Off-Target Analysis of Zinc Finger Nucleases

city: Worcester

first: Scot

last: Wolfe

address: 364 Plantation Street, LRB 619

department: MCCB

institute: UMass Medical School

summary: Zinc Finger Nucleases (ZFNs) facilitate precise editing of DNA enabling targeted genomic modifications in vivo. ZFNs have been employed to obtain genetically modified plants and animals, and cell-based therapies utilizing ZFNs are undergoing clinical trials. However, many ZFNs display dose-dependent toxicity presumably due to the generation of undesired double stranded breaks at off-target sites within the genome. To evaluate the parameters influencing the functional specificity of ZFNs, we compared the in vivo activity of ZFN variants targeting the zebrafish kdrl locus, which display both high on-target activity and dose-dependent toxicity. We evaluated their functional specificity by assessing lesion frequency at 141 potential off-target sites within the zebrafish genome using Illumina sequencing.  Only a minority of these off-target sites displayed significant lesion frequency with kdrl ZFNs. Furthermore, we find that active off-target sites appear to be defined by the thermodynamics of zinc finger-DNA recognition. Surprisingly, we observed that the zinc finger protein specificity and the choice of the engineered dimerization domain of the FokI nuclease could independently influence the fidelity of these ZFNs. The results of this study have implications for the assessment of likely off-target sites within a genome and point to both ZFP-dependent and –independent mechanisms of potential improvement for engineering ZFNs with higher levels of precision.

overall_design:
Examined lesions at 141 off-target sites for various treatments of ZFNs and compare to the untreated sample
stage 1: raw read but missing quality values
stage 2: fastq files available from SRA

first: Ankit

last: Gupta


title: Genome-wide Measurement of RNA Secondary Structure in Yeast

status: Public on Aug 24 2010

city: Stanford

first: Michael

last: Kertesz

address: 318 Campus Dr.

institute: Stanford University

summary: The structures of RNA molecules are often important for their function and regulation, yet there are no experimental techniques for genome-scale measurement of RNA structure. Here, we describe a novel strategy termed Parallel Analysis of RNA Structure (PARS), which is based on deep sequencing fragments of RNAs that were treated with structure-specific enzymes, thus providing simultaneous in-vitro profiling of the secondary structure of thousands of RNA species at single nucleotide resolution. We apply PARS to profile the secondary structure of the mRNAs of the budding yeast S. cerevisiae and obtain structural profiles for over 3000 distinct transcripts. Analysis of these profiles reveals several RNA structural properties of yeast transcripts, including the existence of more secondary structure over coding regions compared to untranslated regions, a three-nucleotide periodicity of secondary structure across coding regions, and a relationship between the efficiency with which an mRNA is translated and the lack of structure over its translation start site. PARS is readily applicable to other organisms and to profiling RNA structure in diverse conditions, thus enabling studies of the dynamics of secondary structure at a genomic scale.

overall_design:
RNA sample was treated with one of two structure-specific enzymes (RNase V1 or RNase S1). Four independent V1 experiments and three independent S1 experiments were carried out.

Processed data file linked below.  Data processing involves merging (or rather log-ratio-ing) the 7 lanes of SOLiD sequencing data against each other.
Also linked below are the genome and transcriptome FASTA files used for mapping, and the annotation file having the format: gene_ID, chromosome, start, end, feature. Start and end are 1-based; feature is "Transcript" for the entire transcript (including introns), "Intron", "Exon", "5UTR" or "3UTR".

Genome-wide measurement of RNA secondary structure in yeast, Kertesz et al., Nature Volume:467, Pages:103-107, Date published:(02 September 2010)
http://www.nature.com/nature/journal/v467/n7311/abs/nature09322.html

first: Yue

last: Wan

first: Elad

last: Mazor

first: John

last: Rinn

first: Robert

middle: C

last: Nutter

first: Howard

last: Chang

first: Eran

last: Segal


title: Control of Embryonic Stem Cell State by Mediator and Cohesin (Illumina ChIP-Seq data)

status: Public on Aug 12 2010

city: Cambridge

first: Richard

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: The key transcription factors that control the embryonic stem cell gene expression program have been identified, but how they function to implement this program is not well understood.  While screening for genes essential for maintenance of ES cell state, we identified many components of the Mediator and Cohesin complexes.  Mediator and Cohesin were found to physically and functionally connect the enhancers and core promoters of active genes.  An ES cell Mediator complex was found to copurify with Cohesin and its loading factor Nipbl, and normal levels of these proteins were essential for expression of the genes they occupy and for maintenance of ES cell state.

overall_design:
See associated publication.

Sample GSM555166 (GSE22320) was used as a negative control.

middle: H

last: Kagey

first: Steve

last: Bilodeau

first: Jamie

last: Newman

first: David

last: Orlando


title: Control of Embryonic Stem Cell State by Mediator and Cohesin

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

overall_design:
Refer to individual Series
See associated publication.


title: modENCODE_White Lab: genome-wide ChIP data of K4me3 from Kc on Illumina Genome Analyzer.

status: Public on Aug 11 2010

first: Kevin

last: White

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor K4me3 from Kc generated by ChIP and analyzed on Illumina Genome Analyzer.

Keywords: Epigenetics

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:
A validated dataset is comprised of three biological replicates for ChIP-chip experiments and two replicates for ChIP-seq and meet the modENCODE quality standards. The control sample is the chromatin Input used for ChIP. Most factors binding profiles are generated by using specific antibodies for the protein of interest. However, some factors have been tagged by GFP in a transgenic line. In that case, ChIP is generated using an anti-GFP antibody.

This submission represents the ChIP-seq component of the study

first: Nicolas

last: Negre

first: Nicholas

last: Bild

middle: P


title: modENCODE_White Lab: genome-wide ChIP data of disco from E8-16h on Illumina Genome Analyzer.

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor disco from E8-16h generated by ChIP and analyzed on Illumina Genome Analyzer.

Keywords: Epigenetics

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


title: ChIP-seq Identification of Weakly Conserved Heart Enhancers

status: Public on Aug 22 2010

city: Berkeley

first: Matthew

middle: James

last: Blow

address: 1 Cyclotron Road

department: Genomics Division

institute: Lawrence Berkeley National Laboratory

summary: Accurate control of tissue-specific gene expression plays a pivotal role in heart development.  However, few cardiac transcriptional enhancers have thus far been identified. Extreme non-coding sequence conservation successfully predicts enhancers active in many tissues, but fails to identify substantial numbers of enhancers active in the heart.  We used ChIP-seq with the enhancer-associated protein p300 from mouse embryonic heart tissue to identify over three thousand candidate heart enhancers genome-wide.  In contrast to other studied tissues at this time-point, most candidate heart enhancers are not deeply conserved in vertebrate evolution.  Nevertheless, the testing of 130 candidate regions in a transgenic mouse assay revealed that most of them reproducibly function as enhancers active in the heart, irrespective of their degree of evolutionary constraint.  These results provide evidence for tissue-dependent differences in evolutionary constraint of enhancers acting through the transcriptional co-activator p300 at this time-point, and identify a large population of poorly conserved heart enhancers.

overall_design: Examination of p300 binding in embryonic stage 11.5 mouse heart and midbrain

first: Axel

last: Visel

first: Len

last: Pennacchio


title: Comprehensive comparative analysis of strand-specific RNA sequencing methods

status: Public on Aug 15 2010

first: Joshua

last: Levin

address: 320 Charles Street

institute: Broad Institute of MIT & Harvard

summary: Strand-specific massively-parallel cDNA sequencing (RNA-Seq) is a powerful tool for novel transcript discovery, genome annotation, and expression profiling.  Despite multiple published methods for strand-specific RNA-Seq, no consensus exists as to how to choose between them.  Here, we developed a comprehensive computational pipeline for the comparison of library quality metrics from any RNA-Seq method.  Using the well-annotated Saccharomyces cerevisiae transcriptome as a benchmark, we compared seven library construction protocols, including both published and our own novel methods.  We found marked differences in complexity, strand-specificity, evenness and continuity of coverage, agreement with known annotations, and accuracy for expression profiling. Weighing each method’s performance and ease, we identify the dUTP second strand marking and the Illumina RNA ligation methods as the leading protocols, with the former benefitting from the availability of paired-end sequencing.  Our analysis provides a comprehensive benchmark, and our computational pipeline is applicable for assessment of future protocols in any organism.

overall_design: Examination of 11 different strand-specific RNA-Seq libraries from 7 distinct methods; also 2 control non-strand-specific RNA-Seq libraries. To assess the performance of each strand-specific library in digital expression profiling, we compared them to reference expression measurements estimated from expression profiles using competitive hybridization of a mid-log RNA sample vs. genomic DNA using Agilent arrays.

first: Moran

last: Yassour

first: Aviv

last: Regev


title: Genome wide trimethyl-H3K27 distibution in macrophages from wild-type and Jmjd3-/- macrophages.

city: Kyoto

first: Osamu

last: Takeuchi

state: Kyoto

address: Yoshida-konoe-cho, Sakyo-ku,

department: Grad School of Medicine

country: Japan

institute: Kyoto University

summary: Jmjd3 is trimethyl H3K27 specific demethylase required for M2 macrophage polarization. Genomic fragments obtained from wild-type and Jmjd3-/- mouse macrophages were immunoprecipitated with anti H3K27me3 Ab, and deep sequencing was performed.

overall_design: wild-type and Jmjd3-/- macrophages

first: Takashi

last: Satoh


title: Genome-wide profiling of p63 binding sites identifies genes and regulatory elements for p63-related disorders

first: Jo

middle: Huiqing

last: Zhou

address: Geert Grooteplein 26-28

department: Human Genetics

institute: NCMLS

summary: We identified p63 target genes and binding sites responsible for ectodermal defects by genome-wide profiling of p63 binding using ChIP-seq and expression analysis in human primary keratinocytes from patients with p63 mutations. As proof of principle, we identified a novel de novo microdeletion causing limb defects (SHFM1) that includes a p63 binding site functioning as a cis-regulatory element to control expression of the distally located DLX5/DLX6 genes essential for limb development. Our data demonstrate that target genes and regulatory elements detected in this study can serve as powerful tools to identify causative mutations of unresolved ectodermal disorders.

overall_design: ChIP-seq profiles of p63 in primary human keratinocytes established from two different normal individuals.

first: Tuula

last: Rinne

first: Evelyn

middle: N

last: Kouwenhoven

first: Simon

last: van Heeringen

first: Martin

last: Oti

first: Juan

last: Tena

first: M

middle: E

last: Alonso

first: Elisa

last: de la Calle-Mustienes

first: Lilian

last: Parsaulian

first: Leonie

last: Smeenk

first: Emine

last: Bolat

first: Bas

last: Dutilh

first: Martijn

last: Huynen

first: Christian

last: Gilissen

first: Alexander

last: Hoischen

first: Joris

last: Veltman

first: Sandra

last: Tjabringa

first: Joost

last: Schalkwijk

first: Ben

last: Hamel

first: Han

middle: G

last: Brunner

first: Tony

last: Roscioli

first: Emily

last: Oates

first: Meredith

last: Wilson

first: Miguel

last: Manzanares

first: José

last: Gómez-Skarmeta

first: Hendrik

last: Stunnenberg

first: Marion

last: Lohrum

first: Hans

last: van Bokhoven

first: Huiqing


title: modENCODE_White Lab: genome-wide ChIP data of kni from E8-16h on Illumina Genome Analyzer.

first: Kevin

middle: P.

last: White

institute: University of Chicago

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor kni from E8-16h generated by ChIP and analyzed on Illumina Genome Analyzer.

Keywords: Epigenetics

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

first: Nicolas

last: Negre

first: Nicholas

last: Bild


title: Chip-seq of H3 in murine embryonic stem cells, myotubes and pro-B cells.

first: Richard

middle: A

last: Young

summary: Nucleosome remodeling results in loss of histone occupancy.  To gain insight into variations in H3 occupancy in different murine cell types, chromatin immunoprecipitation coupled with massive parallel sequencing (ChIP-seq) was performed to determine genome wide occupancy of H3 in ES cells, myotubes and pro-B cells.

overall_design: DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing.  ChIP was performed using an antibody against total H3 in murine ES cells in normal culture conditions, murine ES cells treated with the TGF-beta inhibitor (SB431542, 10uM) for 24 hours, myotubes differentiated for 48 hours and pro-B cells under normal culture conditions.

first: Alan

last: Mullen


title: modENCODE_White Lab: genome-wide ChIP data of Trl-D2 from Kc on Illumina Genome Analyzer.

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor Trl-D2 from Kc generated by ChIP and analyzed on Illumina Genome Analyzer.

Keywords: Epigenetics

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


title: Expression profiling of small RNAs in control and H2O2-treated rice seedlings

city: Beijing

first: Tian

last: Li

address: Chinese Academy of Agricultural Sciences

institute: Institute of Crop Science

summary: We aimed to identify putative H2O2-regulated miRNAs expressed in rice seedlings under oxidative stress by using a deep sequencing approach developed by Solexa (Illumina). Two small RNA libraries were constructed from H2O2-treated and control rice seedlings, and more than five million small RNA sequence reads were generated for each library. We identified seven H2O2-responsive miRNA families via expression profiling of the miRNAs based on a comparative miRNAomic analysis in combination with experimental validation. Furthermore, 32 miRNAs, 17 from known miRNA loci and 15 from novel miRNA loci, were also newly identified from the sequencing data. To the best of our knowledge, this is the first report of a systematic investigation of H2O2-regulated miRNAs and their targets in plants.

overall_design: Examination of 2 different small RNA expression profilings in the control and H2O2 treated rice samples.

first: Jin-Yuan

last: Liu


title: Transcriptome sequencing and analysis of two ants: Camponotus floridanus and Harpegnathos saltator

first: zhiyong

last: huang

summary: Deep sequencing of mRNA from two Ants: Camponotus floridanus and Harpegnathos saltator

overall_design: Analysis of poly(A)+ RNA of different specimens: egg,larva,male,minor and major for Camponotus floridanus while egg,larva,male,worker and gammergate for Harpegnathos saltator

first: Shelley

middle: L

last: Berger

first: Danny

last: Reinberg

first: Jun

last: Wang

first: Jürgen

last: Liebig


title: modENCODE_White Lab: genome-wide ChIP data of Pcl from E0-8h on Illumina Genome Analyzer.

address: 900 E. 57th STR. 10th FL.

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor Pcl from E0-8h generated by ChIP and analyzed on Illumina Genome Analyzer.

Keywords: Epigenetics

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


title: Genome-wide analysis of insulin-like growth factor 1 receptor (IGF1R) binding sites in DFB cells

city: Montreal

first: Ali

last: Tofigh

state: Quebec

address: McGill Centre for Bioinformatics , Life Sciences Complex, Bellini Building, room 435, 3649 Promenade Sir-William-Osler

institute: McGill University

summary: The insulin-like growth factor 1 receptor (IGF-1R) plays crucial roles in developmental and cancer biology. Most of its biological effects have been ascribed to its tyrosine kinase activity. We report that IGF-1 promotes the modification of IGF-1R by small ubiquitin-like modifier protein-1 (SUMO-1) and its translocation to the nucleus. Nuclear IGF-1R associated with enhancer-like elements and increased transcription in reporter assays. We used ChIP-seq to examine the interaction of IGF-1R with DNA on a genome-wide scale. Analysis of the data set resulted in 568 candidate peaks, that is, statistically significant IGF-1R-enriched regions. The IGF-1R-enriched regions were divided into five classes on the basis of their location relative to known genes. Most of the IGF-1R-interacting sites (80%) were located distal from any annotated gene (intergenic), 6.3% were located in introns, 6.3% in exons, 3.4% were <20 kb upstream of an annotated transcript start site (5'UTR + 20 kb upstream), and 3.6% were <20 kb downstream of an annotated transcript end site (3'UTR + 20 kb downstream).

overall_design: Analysis of the genomic interaction of IGF1R in DFB cells

first: Bita

last: Sehat

first: Yingbo

last: Lin

first: Eric

last: Trocmé

first: Ulrika

last: Liljedahl

first: Jens

last: Lagergren

first: Olle

last: Larsson


title: modENCODE_White Lab: genome-wide ChIP data of Trl from E16-24h on Illumina Genome Analyzer.

city: Chicago

first: Kevin

last: White

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor Trl from E16-24h generated by ChIP and analyzed on Illumina Genome Analyzer.

Keywords: Epigenetics

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

first: Nicolas

last: Negre

first: Nicholas

last: Bild


title: modENCODE_White Lab: genome-wide ChIP data of CBP from E0-4h on Illumina Genome Analyzer.

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor CBP from E0-4h generated by ChIP and analyzed on Illumina Genome Analyzer.

Keywords: Epigenetics

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


title: modENCODE_White Lab: genome-wide ChIP data of 3dFemale from 7T on Illumina Genome Analyzer.

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor 3dFemale from 7T generated by ChIP and analyzed on Illumina Genome Analyzer.

Keywords: Epigenetics

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


title: modENCODE_White Lab: genome-wide ChIP data of GFP from 10T-E16-24h on Illumina Genome Analyzer.

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor GFP from 10T-E16-24h generated by ChIP and analyzed on Illumina Genome Analyzer.

Keywords: Epigenetics

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


title: Deep sequencing discovery of novel and conserved microRNAs in trifoliate orange (Citrus trifoliata)

first: Changnian

last: Song

address: Weigang No.1

department: College of Horticulture

institute: Nanjing Agricultural University

summary: MicroRNAs (miRNAs) play a critical role in post-transcriptional gene regulation.  miRNAs have been shown to control many genes involved in various biological and metabolic processes. Deep sequencing technologies have facilitated identification of species-specific or lowly expressed as well as conserved or highly expressed miRNAs in plants. In this research, we used Solexa sequencing to discover new microRNAs in trifoliate orange (Citrus trifoliata) an important rootstock of citrus. A total of 13,106,753 reads representing 4,876,395 distinct sequences were obtained from a short RNA library generated from small RNA extracted from C. trifoliata flower and fruit tissues, Based on sequence similarity and hairpin structure prediction, we found that 178,102 reads representing 89 sequences from 42 highly conserved miRNA families, have perfect matches to known miRNAs. We also identified 10 novel miRNA candidates, whose precursors were all potentially generated from citrus ESTs. And of them five miRNA* sequences were also sequenced. These sequences had not been described in other plant species and accumulation of these 10 novel miRNAs were confirmed by qRT-PCR analysis.  Potential target genes were predicted for most conserved and novel miRNAs. Moreover, four target genes included one encoding IRX12 copper ion binding/ oxidoreductase and three genes encoding NB-LRR disease resistance protein have been experimentally verified by detection of the miRNA-mediated mRNA cleavage in C. trifoliata.

overall_design: Size fractionated small RNAs (16-30 bp) from total RNA extracts was ligated to 5' and 3' adapters, and reverse transcribed. After PCR amplification the sample was subjected to Solexa sequencing. The resultant 35nt sequence data were filtered according to base quality value. The remained sequences were used to trim 5' and 3' adaptors. The clean tags were used for further analysis.

first: Jinggui

last: Fang


title: modENCODE_White Lab: genome-wide ChIP data of GFP from 10T-W3L on Illumina Genome Analyzer.

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor GFP from 10T-W3L generated by ChIP and analyzed on Illumina Genome Analyzer.

Keywords: Epigenetics

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


title: genome-wide measurement of mRNA lifetime in Escherichia coli

status: Public on Jul 30 2010

first: Huiyi

last: Chen

address: 12 Oxford St

department: Chemistry

institute: Harvard University

summary: We measured the mRNA abundance in E.coli using RNAseq to calculate mRNA lifetimes. The data is used in support of a larger paper on the proteome and transcriptome of E.coli.

overall_design:
Comparison of mRNA abundance over time, after the addition of transcription inhibitor, rifampicin.
Center: Harvard University

first: Sunney

last: Xie


title: modENCODE_White Lab: genome-wide ChIP data of disco from E0-8h on Illumina Genome Analyzer.

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor disco from E0-8h generated by ChIP and analyzed on Illumina Genome Analyzer.
Keywords: Epigenetics

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


title: Analysis of mir-223 knockout cultured neutrophils versus wild-type cultured neutrophils, by ribosome profiling and mRNA-Seq

status: Public on Aug 03 2010

city: Singapore

first: Huili

last: Guo

address: 28 Medical Drive

country: Singapore

institute: National University of Singapore

summary: MicroRNAs (miRNAs) are endogenous ~22-nucleotide RNAs that mediate important gene-regulatory events by pairing to the mRNAs of protein-coding genes to direct their repression. Repression of these regulatory targets leads to decreased translational efficiency and/or decreased mRNA levels, but the relative contributions of these two outcomes have been largely unknown, particularly for endogenous targets expressed at low-to-moderate levels. Here, we use ribosome profiling to measure the overall effects on protein production and compare these to simultaneously measured effects on mRNA levels. For both ectopic and endogenous miRNA regulatory interactions, lowered mRNA levels account for most (≥84%) of the decreased protein production. These results show that changes in mRNA levels closely reflect the impact of miRNAs on gene expression and indicate that destabilization of target mRNAs is the predominant reason for reduced protein output.

overall_design:
Examine ribosome footprints and mRNA abundance of mir-223 knockout cultured neutrophils, versus wild-type cultured neutrophils

Supplementary processed data file linked below.
mir223_summaryTable.txt: log2 fold changes (miR-223-knockout versus wild-type neutrophils).

first: H

first: N

middle: T

last: Ingolia

first: J

last: Weissman

first: D

last: Bartel


title: ChIP-Seq of Histone Methylation and RNAP2 in Human Jurkat cells.

status: Public on Jul 24 2010

first: Richard

last: Young

summary: Three transcriptional states can be defined by histone modifications and RNA polymerase II enriched at promoters and across the body of genes.  To gain insight into the active, poised and silent genes in human T-ALL cells, two antibodies against RNAP2, and  antibodies against H3K4me3, H3K79me2, and H3K27me3 were used for chromatin immunoprecipitation coupled with massive parallel sequencing (ChIP-seq).

overall_design: Genomic DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing.  ChIP was performed using an antibody against RNAP2, H3K4me3, H3K79me2, and H3K27me3 using whole cell extract (WCE) as a background control.  ChIP was performed using a two antibody against hypophosphorylated forms of RNAP2 in two biological replicates. All other ChIPs were done in biological replicates with a single lane of sequencing.

first: Lee

last: Lawton

first: Zi-Peng

last: Fan


title: Mammalian microRNAs predominantly act to decrease target mRNA levels

summary:
MicroRNAs (miRNAs) are endogenous ~22-nucleotide RNAs that mediate important gene-regulatory events by pairing to the mRNAs of protein-coding genes to direct their repression. Repression of these regulatory targets leads to decreased translational efficiency and/or decreased mRNA levels, but the relative contributions of these two outcomes have been largely unknown, particularly for endogenous targets expressed at low-to-moderate levels. Here, we use ribosome profiling to measure the overall effects on protein production and compare these to simultaneously measured effects on mRNA levels. For both ectopic and endogenous miRNA regulatory interactions, lowered mRNA levels account for most (≥84%) of the decreased protein production. These results show that changes in mRNA levels closely reflect the impact of miRNAs on gene expression and indicate that destabilization of target mRNAs is the predominant reason for reduced protein output.

This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series.


title: modENCODE_White Lab: genome-wide ChIP data of hkb from E8-16h on Illumina Genome Analyzer.

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor hkb from E8-16h generated by ChIP and analyzed on Illumina Genome Analyzer.

Keywords: Epigenetics

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


title: modENCODE_White Lab: genome-wide ChIP data of Sin3A from E0-12h on Illumina Genome Analyzer.

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor Sin3A from E0-12h generated by ChIP and analyzed on Illumina Genome Analyzer.

Keywords: Epigenetics

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


title: ENCODE Caltech RNA-seq

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
This data was produced by the Wold lab at Caltech as part of the ENCODE Project. RNA-Seq is a method for mapping and quantifying the transcriptome of any organism that has a genomic DNA sequence assembly. RNA-Seq is performed by reverse-transcribing an RNA sample into cDNA, followed by high throughput DNA sequencing. The resulting sequence reads are then informatically mapped onto the genome sequence.
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: The transcriptome measurements shown on these tracks were performed on polyA selected RNA from total cellular RNA. Data have been produced in two formats: single reads, each of which comes from one end of a randomly primed cDNA molecule; and paired-end reads, which are obtained as pairs from both ends cDNAs resulting from random priming. The resulting sequence reads are then informatically mapped onto the genome sequence (Alignments). Those that don't map to the genome are mapped to known RNA splice junctions (Splice Sites). These mapped reads are then counted to determine their frequency of occurrence at known gene models. Sequence reads that cluster at genome locations that lack an existing transcript model are also identified informatically and they are quantified. RNA-Seq is especially suited for giving information about RNA splicing patterns and for determining unequivocally the presence or absence of lower abundance class RNAs. As performed here, internal RNA standards are used to assist in quantification and to provide internal process controls. This RNA-Seq protocol does not specify the coding strand. As a result, there will be ambiguity at loci where both strands are transcribed. The "randomly primed" reverse transcription is, apparently, not fully random. This is inferred from a sequence bias in the first residues of the read population, and this likely contributes to observed unevenness in sequence coverage across transcripts. These tracks show 1x32 n.t. or 2x75 n.t. sequence reads of cDNA obtained from biological replicate samples (different culture plates) of the ENCODE cell lines. The 32 n.t. sequences were aligned to the human genome (hg18) and UCSC known-gene splice junctions using different sequence alignment programs. The 2x75 n.t. reads were mapped serially, first with the Bowtie program (Langmead et al., 2009) against the genome and UCSC known-gene splice junctions (Splice Sites). Bowtie-unmapped reads were then mapped using BLAT to find evidence of novel splicing, by requiring at least 10 bp on the short-side of the splice.

first: Barbara

last: Wold

last: Myers

first: Ali

last: Mortazavi

first: Brian

last: Williams

first: Diane

last: Trout

first: Brandon

last: King

first: Ken

last: McCue

first: Lorian

last: Schaeffer

first: Norma

last: Neff

first: Florencia

last: Pauli

first: Fan

last: Zhang

first: Tim

last: Reddy

first: Rami

last: Rauch

first: Gary

last: Schroth

first: Shujun

last: Luo

first: Eric

last: Vermaas


title: Deletion of Tardbp Down-Regulates Tbc1d1, a Gene Linked to Obesity, and Alters Body Fat Metabolism

status: Public on Jul 15 2010

city: Baltimore

first: Jonathan

last: Ling

address: 720 Rutland Ave.

department: Neuropathology

institute: Johns Hopkins University

summary: Tat Activating Regulatory DNA Binding Protein (Tardbp or TDP-43), a highly conserved metazoan DNA/RNA binding protein thought to be involved in RNA transcription and splicing, has been linked to the pathophysiology of amyotrophic lateral sclerosis and frontotemporal lobar degeneration and is essential for early embryonic development.  However, neither the physiological role of TDP-43 in the adult nor its downstream targets are well defined.  To address these questions, we developed conditional Tardbp knockout mice and embryonic stem (ES) cell models.  Here, we show that post-natal deletion of Tardbp in mice caused dramatic loss of body fat followed by rapid death.  Moreover, conditional Tardbp knockout ES cells failed to proliferate.  Importantly, high throughput DNA sequencing analysis on the transcriptome of ES cells lacking Tardbp revealed a set of downstream targets of TDP-43.  We show that Tbc1d1, a gene known to mediate leanness and linked to obesity, is down-regulated in the absence of TDP-43.  Collectively, our results establish that TDP-43 is critical for fat metabolism and ES cell survival.

overall_design: One allele of both iTDPKO and cTDP ES cells were replaced by CAG-ErCreEr.  The other allele in iTDPKO ES cells is floxed exon3 while in the cTDP ES cells is wild type.

first: Po-Min

last: Chiang

first: Yun-Ha

last: Jeong

first: Donald

last: Price

first: Susan

last: Aja

first: Philip

last: Wong


title: Regulatory Divergence in Drosophila revealed by mRNA-seq (trans-splicing)

status: Public on Jul 20 2010

city: Farmington

first: Brenton

middle: R

last: Graveley

address: 400 Farmington Avenue

department: Genetics and Genome Sciences

institute: University of Connecticut Health Center

summary:
Deep Sequencing of mRNA from Drosophila melanogaster, Drosophila Sechellia, and their F1 hybrid.

These data were generated in a study to analyze the extent and specificity of trans-splicing in Drosophila. mRNA-seq libraies were prepared from poly(A)+ RNA prepared from whole F1 hybrids of D. melanogaster and D. sechellia (female 0-3d post eclosion). Separate control libraries were prepared from D. melanogaster and D. sechellia total RNA (mixed before library preparation). The results of this study identified 80 novel trans-splicing events between homologous alleles of the same gene.

Keywords: RNA-Seq

Keywords: Expression profiling by high throughput sequencing

sample_organism: Drosophila melanogaster x Drosophila sechellia

overall_design: There were 2 total samples in this study.  Paired-end mRNA-seq was used to survey trans-splicing in F1 hybrids of D. melanogaster and D. sechellia.  A mixed "control" library was used to assess the frequency of false-positive trans-splicing signal resulting from errors in reference genomes, high-throughput sequencing, and RT-PCR amplification based strand-switching.

first: C

last: McManus


title: Deep Sequencing of Human Nuclear and Cytoplasmic Small RNAs Reveals an Unexpectedly Complex Subcellular Distribution of miRNAs and tRNA 3' Trailers

status: Public on Jul 14 2010

city: Guangzhou

first: Jian-You

last: Liao

address: XinGang West Road

institute: Sun Yat-Sen University

summary: Background: MicroRNAs (miRNAs) are 22-nt small non-coding regulatory RNAs that have generally been considered to regulate gene expression at the post-transcriptional level in the cytoplasm. However, recent studies have reported that some miRNAs localize to and function in the nucleus. Methodology/Principal Findings: To determine the number of miRNAs localized to the nucleus, we systematically investigated the subcellular distribution of small RNAs (sRNAs) by independent deep sequencing the nuclear and cytoplasmic pools of 18- to 30-nucleotide sRNAs from human cells. We identified 339 nuclear and 324 cytoplasmic known miRNAs, 300 of which overlap, suggesting that the majority of miRNAs are imported into the nucleus. With the exception of a few miRNAs evidently enriched in the nuclear pool, such as the mir-29b, the ratio of miRNA abundances in the nuclear fraction versus in the cytoplasmic fraction vary to some extent. Moreover, our results revealed that a large number of tRNA 3' trailers are exported from the nucleus and accumulate in the cytoplasm. These tRNA 3' trailers accumulate in a variety of cell types, implying that the biogenesis of tRNA 3' trailers is conserved and that they have a potential functional role in vertebrate cells. Conclusion/Significance: Our results provide the first comprehensive view of the subcellular distribution of diverse sRNAs and new insights into the roles of miRNAs and tRNA 3' trailers in the cell

overall_design: Discovery and characterization of small RNA species through deep sequencing of nuclear and cytoplasmic small RNA fractions from 5-8F cells, a nasopharyngeal carcinoma cell line.

first: Liang-Hu

last: Qu


title: The mental retardation gene PHF8 mediates histone H4K20/H3K9 demethylation and regulates zebrafish brain apoptosis and craniofacial development: ChIP-Seq analysis

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

summary: PHF8 (PHD Finger 8) mutations have been found in patients with X-linked mental retardation (XLMR) and craniofacial deformities. Here we identify PHF8 as the first enzyme that mediates demethylation of mono-methylated histone H4 lysine (K) 20 (H4K20me1), with additional activities towards H3K9me2/1 and H3K27me2. Patient mutations significantly compromise the demethylase activity, indicating functional importance. ChIP-seq identified PHF8 near the transcription start sites (TSS) of over 7000 target genes as well as in gene bodies and intergenic regions. PHF8 depletion resulted in up-regulation of H4K20me1 and H3K9me1 at the TSS-associated sites, and H3K9me2 in the gene bodies and intergenic regions, respectively, demonstrating differential substrate specificities at different target genomic locations. PHF8 depletion at the TSS results in decreased target gene expression, which is coincident with increased occupancy of the protein L3MBTL1 previously shown to induce chromatin compaction via binding to lower methyl states including H4K20me1 and H3K9me1.

overall_design: HeLa cells stably expressing control and PHF8 shRNA were used to profile the histone modifications including H4K20me1, H3K9me1 and 2 by ChIP-seq. For PHF8 ChIP-seq, chromatin was obtained by formaldehyde cross-link and sonication. For chIP-seq of Histone modifcation, chromatin was prepared by MNase digestion to obtain mono-nucleosomes.

first: Hank

last: Qi

first: Madathia

last: Sarkissian

first: Gangq-Qing

first: Zhibin

last: Wang

first: Arindam

last: Bhattacharjee

first: D

last: Gordon

first: Michelle

last: Gonzales

first: Fei

last: Lan

first: Pat

last: Ongusaha

first: Maite

last: Huarte

first: Nasser

middle: K

last: Yaghi

first: Huijun

last: Lim

first: Benjamin

last: Garcia

first: Leonardo

last: Brizuela

first: Keji

last: Zhao

first: Thomas

middle: M

last: Roberts

first: Yang

last: Shi


title: SplicePL: de novo splice junction detection from paired-end RNA-seq reads

status: Public on Jul 13 2010

city: Philadelphia

first: Lifeng

last: Tian

state: PA

address: 422 Curie Bldv

institute: University of Pennsylvania

summary: We generate this 130-nt dataset to benchmark SplicePL, TopHat and SpliceMap.

overall_design: Retina sample from one human donor.

first: Dwight

last: Stambolian


title: Identification of Primary Gene Targets of TFAP2C in Hormone Responsive Breast Carcinoma Cells

city: Iowa City

last: Bair

state: IA

address: 335 EMRB

institute: University of Iowa

summary: To develop a more complete characterization of TFAP2C target genes, ChIP-seq with anti-TFAP2C antibody and expression arrays with TFAP2C knock down were analyzed in MCF-7 breast carcinoma cells.

overall_design: To find TFAP2C binding sites

first: George

middle: W

last: Woodfield

first: Yizhen

last: Chen

first: Frederick

last: Domann

first: Ronald

middle: J

last: Weigel


title: ChIP-Seq data for histone marks in estrogen-inducible MyoD1 fibroblasts

first: Richard

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: The conversion of fibroblasts to myotubes by forced expression of MyoD1 is among the earliest demonstrations of reprogramming of vertebrate cell state.   To gain insights into the chromatin state of genes required for reprogramming, we profiled H3K4me3, H3K27me3 and H3K9me3.

overall_design: DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing. ChIP was performed using an antibody against H3K4me3, H3K27me3 and H3K9me3.

first: Steve

last: Bilodeau


title: Traf6 function in the innate immune response of zebrafish embryos

status: Public on Aug 01 2010

city: Amsterdam

first: Oliver

last: Stockhammer

state: NH

address: Meibergdreef 15

department: Medical Microbiology

institute: AMC

summary: Transcriptional profiling of the zebrafish embryonic host response to a systemic bacterial infection with Salmonella typhimurium (strain SL1027); comparison between traf6 knock-down and control morpholino treated embryos.

overall_design: All infection experiments were performed using mixed egg clutches of ABxTL strain zebrafish. Embryos injected with traf6 morpholino or a 5bp mismatch control morpholino were staged at 27 hours post fertilization (hpf) by morphological criteria and approximately 250 cfu of DsRed expressing Salmonella bacteria were injected into the caudal vein close to the urogenital opening. As a control an equal volume of PBS was likewise injected. Pools of 20-40 infected and control embryos were collected 8 hours post infection (hpi). The whole procedure was preformed in triplicate on separate days. Total RNA of the biological triplicates was pooled using equal amounts of RNA prior to RNAseq library preparation.

first: O

first: H

last: Rauwerda

first: F

last: Wittink

first: T

last: Breit

first: A

last: Meijer

last: Spaink


title: microRNA expression in human tonsillar B cell populations

city: bethesda

first: Seolkyoung

last: Jung

address: 10 Center Dr

department: NIAMS

institute: NIH

summary: small RNA profiles of 6 human tonsillar B cell populatios (naive B cells, pre-germinal center B cells, centrocytes, centroblasts, memory B cells, and plasma cells) were determined by deep sequencing.  These samples were compared to mouse developing lymphocytes, various hematopoietic cell lineages, and tissues.

overall_design: small RNA expression profiles of 6 well defined B cell populations isolated from human tonsils.

first: Stefan

last: Kuchen

first: Wolfgang

last: Resch

first: Arito

last: Yamane

last: Kuo

first: Zhiyu

last: Li

first: Tirtha

last: Chakraborty

first: Lai

last: Wei

first: Arian

last: Laurence

first: Tomoharu

last: Yasuda

first: Siying

last: Peng

first: Jane

last: Hu-Li

first: Kristina

last: Lu

first: Wendy

last: Dubois

first: Yoshiaki

last: Kitamura

first: Nicolas

last: Charles

first: Hong-wei

last: Sun

last: Muljo

first: Pamela

last: Schwartzberg

first: William

last: Paul

first: John

last: O'Shea

first: Klaus

last: Rajewsky

first: Rafael

last: Casellas


title: RNA-seq analysis of the transcriptome from Sulfur Deprivation Chlamydomonas cells

status: Public on Jul 08 2010

first: Arthur

last: Grossman

address: 260 Panama Street

department: Plant Biology

institute: Carnegie Institute for Science

summary:
The Chlamydomonas reinhardtii transcriptome was characterized from nutrient-replete and sulfur-depleted wild-type and snrk2.1 mutant cells; the mutant is null for the regulatory serine-threonine kinase SNRK2.1, which is required for acclimation to sulfur deprivation. The transcriptome analyses involved microarray hybridization and RNA-seq technology; RT-qPCR evaluation of the data obtained by these techniques showed that RNA-seq is significantly more quantitative than microarray hybridizations. Sulfur-deprivation-responsive transcripts included those encoding proteins involved in sulfur acquisition and assimilation, recycling of sulfur-containing amino acids, synthesis of reduced sulfur metabolites and cofactors, and modification of cellular structures such as the cell wall and complexes associated with the photosynthetic apparatus. Moreover, the data suggest that cells deprived of sulfur favors accumulation of proteins with fewer sulfur-containing amino acids. Most of these sulfur-deprivation responses are controlled by the SNRK2.1 kinase. Furthermore, the snrk2.1 mutant exhibits a set of unique responses during both sulfur-replete and sulfur-depleted conditions that are not observed in wild-type cells. Many of these responses are likely to be elicited by singlet O2 accumulation in the mutant cells. The transcriptome results for the wild-type and mutant cells strongly suggest the occurrence of massive changes in cellular physiology and metabolism as the cells become depleted for sulfur, and reveal aspects of acclimation that are likely critical for cell survival.

The three supplementary files GSE17970_supplemental_table_*.xls below include results of the differential expression analysis (expression estimates, fold changes  and p-values), and different clusters of functionally related genes.

overall_design:
Chlamydomonas strains used for this study were D66 (wt strain; nit2 cw15 mt+), ars11 (snrk2.1cw15mt+), 21gr (wt strain; nit5 mt-) and sac1 (sac1mt+). The ars11 strain was designated as the snrk2.1 mutant throughout since the lesion is in the SNRK2.1 gene. Cells were cultured under continuous light of ~60 μmol photon m-2s-1 at 23ºC in liquid and on solid Tris-Acetate-Phosphate (TAP) medium. To impose S deprivation, cells in mid-logarithmic growth phase were washed twice with liquid TAP medium without S (TAP-S), and equal numbers of cells were resuspended in TAP or TAP-S. Cell aliquots were collected for RNA isolation just prior to and 6 h after being transferred to TAP and TAP-S medium.
Total RNA from wt (D66) and snrk2.1 mutant cells after 0 and 6 h of being transferred to -S medium were submitted to Illumina for sequencing using their proprietary Genome Analyzer. cDNA libraries were assembled according to the manufacturer’s RNA-seq protocol, loaded and sequenced as 35-mers in a total of 11 Solexa lanes. Raw image files were collected by the sequencer and analyzed using the standard Solexa pipeline.

first: David

last: Gonzalez-Ballester

last: Casero

first: Shawn

last: Cokus

first: Matteo

last: Pellegrini

first: Sabeeha

middle: S

last: Merchant


title: Regulation of heterochromatic DNA replication by histone H3 lysine 27 methyltransferases

status: Public on Jul 21 2010

city: Dallas

first: Hume

last: Stroud

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern

type: Genome variation profiling by high throughput sequencing

summary: Multiple pathways prevent DNA replication from occurring more than once per cell cycle. These pathways block re-replication by strictly controlling the activity of pre-replication complexes, which assemble at specific sites in the genome called origins. Here we show that mutations in the homologous histone 3 lysine 27 (H3K27) monomethyltransferases, ARABIDOPSIS TRITHORAX-RELATED PROTEIN5 (ATXR5) and ATXR6, lead to re-replication of specific genomic locations.   The vast majority of these locations correspond to transposons and other repetitive and silent elements of the Arabidopsis genome.  These sites also correspond to high levels of H3K27 monomethylation, and mutation of the catalytic SET domain is sufficient to cause the re-replication defect.  Mutation of ATXR5 and ATXR6 also causes upregulation of transposon expression and has pleiotropic effects on plant development.  These results uncover a novel pathway that prevents over-replication of heterochromatin in Arabidopsis.

overall_design: Examination of genomic DNA content in endoreduplicating nuclei in wild type and atxr atxr6 mutant plants

first: Steven

last: Jacobsen


title: Transcriptome analysis of two life cycle stages of Trypanosoma brucei gambiense

status: Public on Jul 22 2010

city: Glasgow

first: Annette

last: MacLeod

address: GBRC, 120 University Place

department: Wellcome Centre for Molecular Parasitology

country: United Kingdom

institute: University of Glasgow

summary: Trypanosoma brucei gambiense is the causative agent of the fatal human disease African sleeping sickness. Here we have compared the transcriptome of two different life cycle stages, the potentially human-infective bloodstream form and the non-human-infective procyclic stage, using digital gene expression (DGE) analysis.

overall_design: Digital gene expression analysis was performed on RNA from 3 biological replicates of bloodstream cultured T.b. gambiense strain STIB 386 and compared to that from 3 biological replicates of procyclic cultured T.b. gambiense strain STIB 386.

first: Nicola

last: Veitch

first: Paul

last: Johnson

first: Urmi

last: Trivedi

first: Sandra

last: Terry

last: Wildridge


title: RNA-seq of pancreatic islets isolated from normal female and pregnant female mice

status: Public on Jul 02 2010

city: San Francisco

first: Hail

last: Kim

state: CA

address: 513 Parnassus avenue HSW1090

department: Diabetes Center

institute: University of California San Francisco

summary: During pregnancy, the energy requirements of the fetus impose changes in maternal metabolism. Increasing insulin resistance in the mother maintains nutrient flow to the growing fetus, while prolactin and placental lactogen counterbalance this resistance and prevent maternal hyperglycemia by driving expansion of the maternal population of insulin-producing beta-cells. However, the exact mechanisms by which the lactogenic hormones drive beta-cell expansion remain uncertain. Here we show that serotonin acts downstream of lactogen signaling to drive beta-cell proliferation. Serotonin synthetic enzyme Tph1 and serotonin production increased sharply in beta-cells during pregnancy or after treatment with lactogens in vitro. Inhibition of serotonin synthesis by dietary tryptophan restriction or Tph inhibition blocked beta-cell expansion and induced glucose intolerance in pregnant mice without affecting insulin sensitivity.  Expression of the Gq-linked serotonin receptor Htr2b in maternal islets increased during pregnancy and normalized just prior to parturition, while expression of the Gi-linked receptor Htr1d increased at the end of pregnancy and postpartum.  Blocking Htr2b signaling in pregnant mice also blocked beta-cell expansion and caused glucose intolerance. These studies reveal an integrated signaling pathway linking beta-cell mass to anticipated insulin need during pregnancy. Modulators of this pathway, including medications and diet, may affect the risk of gestational diabetes.

overall_design: Analysis of poly(A)+ RNA from 3 biological replicates of pancreatic islets isolated from normal female and pregnant female mice

first: Francis

middle: F

last: Lynn

first: Michael

last: German


title: Identification and analysis of expression of novel microRNAs of murine gammaherpesvirus 68

city: Martinsried

first: Gunter

last: Meister

address: Am Klopferspitz 18

department: Center for Integrated Protein Science Munich (CIPSM)

institute: Max Planck Institute of Biochemistry

summary: Murine gammaherpesvirus 68 (MHV-68) is closely related to Epstein-Barr virus (EBV) and Kaposi’s sarcoma-associated herpesvirus (KSHV) and provides a small animal model to study the pathogenesis of gammaherpesvirus (γHV) infections. To completely explore the potential of the MHV-68 system for the investigation of gHV miRNAs, it would be desirable to know the number and expression patterns of all miRNAs encoded by MHV-68. By using small RNA deep sequencing, we systematically investigated the MHV-68 miRNA expression profiles in both lytically and persistently infected cells. In addition to the known nine MHV-68 miRNAs, we identified six novel MHV-68 miRNA genes and analyzed the expression levels of all MHV-68 miRNAs. Furthermore, we also characterized the cellular miRNA expression signatures in MHV-68 infected versus non-infected NIH3T3 fibroblasts and in TPA-treated versus non-treated S11 cells. We found that mmu-mir-15b and mmu-mir-16 are highly upregulated upon MHV-68 infection of NIH3T3 cells, indicating a potential role of cellular miRNAs during MHV-68 infection. Our data will aid to fully explore the functions of gHV miRNAs.

overall_design: A mouse fibroblast cell line infected with/without MHV-68 and a MHV-68 infected mouse B lymphoma cell line treated with/without TPA (4 samples in total) were examined.

first: Jiayun

last: Zhu

first: Martin

last: Strehle

first: Anne

last: Frohn

first: Elisabeth

last: Kremmer

first: Kai

middle: P

last: Höfig

first: Heiko

last: Adler


title: Genome-wide transcription start site determination of Geobacter sulfurreducens under multiple growth conditions

status: Public on Jul 01 2010

city: La Jolla

first: Bernhard

last: Palsson

address: 9500 Gilman Dr.

department: Bioengineering

institute: UCSD

summary: Determine the transcription start sites at 1-bp resolution across the entire G. sulfurreducens genome in multiple growth conditions, including fresh water acetate-fumarate (FWAF) medium, nitrogen limitation and growth on electrode.

overall_design: Special capture of the 5' end of primary transcripts in G. sulfurreducens and sequencing with Illumina Genome Analyzer II.

first: Yu

last: Qiu

first: Byung-Kwan

last: Cho

first: Young-Seoub

last: Park

first: Derek

last: Lovley

middle: O

first: Karsten

last: Zengler


title: Analysis of HeLa cells after transfection with miR-1 or miR-155, by ribosome profiling and mRNA-Seq

first: Huili

last: Guo

address: 28 Medical Drive

institute: National University of Singapore

summary: MicroRNAs (miRNAs) are endogenous ~22-nucleotide RNAs that mediate important gene-regulatory events by pairing to the mRNAs of protein-coding genes to direct their repression. Repression of these regulatory targets leads to decreased translational efficiency and/or decreased mRNA levels, but the relative contributions of these two outcomes have been largely unknown, particularly for endogenous targets expressed at low-to-moderate levels. Here, we use ribosome profiling to measure the overall effects on protein production and compare these to simultaneously measured effects on mRNA levels. For both ectopic and endogenous miRNA regulatory interactions, lowered mRNA levels account for most (≥84%) of the decreased protein production. These results show that changes in mRNA levels closely reflect the impact of miRNAs on gene expression and indicate that destabilization of target mRNAs is the predominant reason for reduced protein output.

overall_design:
Examine ribosome footprints and mRNA abundance of HeLa cells transfected with miR-1 or miR-155, versus mock-transfected cells, at two different time points post-transfection.

Supplementary processed data files linked below.
mir155_summaryTable.txt: log2 fold changes (miR-155-transfected versus mock-transfected HeLa cells, 32hr).
mir1_summaryTable.txt: log2 fold changes (miR-1-transfected versus mock-transfected HeLa cells, 32hr).

first: H

first: N

last: Ingolia

first: J

last: Weissman

first: D

last: Bartel


title: A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity

city: New Haven

first: Antonio

middle: J.

last: Giraldez

state: CT

address: 333 Cedar Street

department: Genetics

institute: Yale University

summary: Here we identify a Dicer-independent miRNA biogenesis pathway that employs the slicer catalytic activity of Argonaute2 (Ago2). To uncover Dicer-independent miRNAs, we sequenced  small RNAs in wild type, maternal-zygotic dicer (MZdicer) and MZago2 mutants, using zebrafish as a model system. We find that, in contrast to other miRNAs, miR-451 levels were increased in MZdicer but drastically reduced in the MZago2 mutants. We show that pre-miR-451 processing requires Ago2 catalytic activity in vivo. MZago2 mutant embryos display delayed erythrocyte maturation that can be rescued by wild type Ago2 or miR-451 duplex but not catalytically dead Ago2. We propose that Ago2-mediated cleavage of a subset of pre-miRNAs, followed by uridylation and trimming, generates functional miRNAs in a Dicer-independent manner.

overall_design: Examination of small RNAs (18 to 35 nucleotides) in 3 different zebrafish genotypes (wild type, MZago2, MZdicer) at 48 hours post-fertilization.

first: Daniel

last: Cifuentes


title: Genome-wide nucleosome position data for 12 yeast species

status: Public on Jul 06 2010

city: Boston

first: Alex

last: Tsankov

address: 155 Bay State

institute: MIT

summary: We mapped nucleosome positions genome-wide in 12 Ascomycetes

sample_organism:
Lachancea waltii
Saccharomyces bayanus
Saccharomyces cerevisiae
Yarrowia lipolytica
Debaryomyces hansenii
Candida albicans
Nakaseomyces glabratus
Naumovozyma castellii
Saccharomyces paradoxus
Kluyveromyces lactis
Saccharomyces mikatae
Lachancea kluyveri NRRL Y-12651

overall_design: Illumina sequencing of mononucleosomal DNA isolated from mid-log cultures grown in rich medium (abbreviated CM, in house recipe)

first: Alexander

first: Oliver

last: Rando

first: Aviv

last: Regev


title: Altered Distributions of SMN-containing GEMs and Mitochondria in Motor Neurons of TDP-43 transgenic Mice

status: Public on Jul 31 2010

first: Jonathan

last: Ling

address: 720 Rutland Ave.

institute: Johns Hopkins University

summary: TDP-43, a DNA/RNA binding protein involved in RNA transcription and splicing has been associated with the pathophysiology of neurodegenerative diseases, including ALS. However, the function of TDP-43 in motor neurons remains undefined. Here, we employ both gain- and loss-of-function approaches to determine roles of TDP-43 in motor neurons. Mice expressing human TDP-43 in neurons exhibited growth retardation and premature death that are characterized by abnormal intranuclear inclusions comprised of TDP-43 and Fused in Sarcoma (FUS), and massive accumulation of mitochondria in TDP-43-negative cytoplasmic inclusions in motor neurons, lack of mitochondria in motor axon terminals and immature neuromuscular junctions. Whereas elevated level of TDP-43 disrupts the normal nuclear distribution of Survival Motor Neuron (SMN)-associated Gemini of coiled bodies (GEMs) in motor neurons, its absence prevents the formation of GEMs in the nuclei of these cells. Moreover, transcriptome-wide deep sequencing analysis revealed that decrease in abundance of neurofilament transcripts contributed to the reduction of caliber of motor axons in TDP-43 mice. In concert, our findings indicate that TDP-43 participates in pathways critical for motor neuron physiology, including those that regulate the normal distributions of SMN-associated GEMs in the nucleus and mitochondria in the cytoplasm.

overall_design: Human TDP-43 coding region were inserted into pThy1.2 expression cassette and subsequently injected into C57BL/6;SJL hybrid mouse embryos to make human TDP-43 transgenic mice

first: Xiu

last: Shan

first: Po-Min

last: Chiang

first: Donald

last: Price

first: Philip

middle: C

last: Wong


title: Genome-wide analysis of siRNA accumulation in Arabidopsis treated with bacteria

status: Public on Jul 23 2010

city: St. Louis

first: Weixiong

last: Zhang

state: MO

address: Campus Box 1045

department: Computer Science and Engineering

institute: Washington University in St. Louis

summary: To identify endogenous siRNAs in response to bacterial pathogen at a whole genome level, we performed small RNA profiling on Pseudomonas syringae-challenged Arabidopsis and obtained more than 24.6 million (M) reads with more than 3.8 M unique small RNAs that perfectly matched Arabidopsis genome. We found some new miRNAs and some miRNA induced by pathogen infection. We also identified more than 20K unique siRNAs from the NAT mRNAs and 22K siRNAs from the introns or intron-exon junction of the NATs.

overall_design: Sequencing of small RNAs from Arabidopsis infected by control and 3 bacterias in 6h and 14h.

first: Hailing

last: Jin

first: Padmanabhan

last: Chellappan

first: Xiang

last: Zhou


title: Genome-wide maps of RAP1 binding sites.

status: Public on Jul 10 2010

city: Madrid

first: Paula

last: Martinez

state: Madrid

address: Melchor Fernandez Almagro 3

country: Spain

institute: CNIO

summary: By performing chromatin immunoprecipitation coupled with ultra-high-throughput sequencing (ChIP-seq), we find that RAP1 binds to telomeres as well as to extra-telomeric sites through the (TTAGGG)2 consensus motif. Extra-telomeric RAP1 binding sites are particularly abundant at subtelomeric regions, and this is in agreement with preferential deregulation of subtelomeric genes in Rap1-deficient cells. Significantly, more than 70% of extratelomeric RAP1 binding sites are located in the vicinity of known genes and about 40% of the genes deregulated in Rap1-null cells contain binding sites for RAP1, suggesting a role of RAP1 in transcriptional control.

overall_design: Examination of RAP1 binding by CHIP-seq in two independent wild-type mefs using as negative control two independent RAP1-deleted mefs

last: Martínez

first: Maria

last: Thanasoula

first: Ana

last: Carlos

first: Gonzalo

last: Gómez

first: Agueda

last: Tejera

first: Stefan

last: Schoeftner

first: Orlando

last: Dominguez

first: David

last: Pisano

first: Madalena

last: Tarsounas

last: Blasco


title: Expanding the MicroRNA Targeting Code:  A Novel Type of Site with Centered Pairing

status: Public on Jun 25 2010

city: Cambridge

first: Jin-Wu

last: Nam

address: Nine Cambridge Center

institute: Whitehead Institute

summary: We present “centered sites,” a class of microRNA target sites that lacks both perfect seed pairing and 3'-compensatory pairing and instead has 11–12 contiguous Watson–Crick pairs to the center of the microRNA.  In elevated Mg2+, centered sites impart mRNA cleavage, but in cells, centered sites repress protein output without consequential Agronaute-catalyzed cleavage.  Our study also identified novel extensively paired sites that are cleavage substrates in cultured cells and human brain.  This expanded repertoire of cleavage targets and the identification of the centered site type help explain why central regions of many microRNAs are evolutionarily conserved.

sample_organism:
Danio rerio
Homo sapiens

platform_organism:
Danio rerio
Homo sapiens

overall_design: To study centered sites and identify miRNA cleavage targets, mRNA degradomes were sequenced from human brain and HeLa cells, and smallRNAs were sequenced from human brain and zebrafish embryo at 24 hours post fertilization (hpf). Replicates were combined before the analysis. Fastq files are not available for GSM548638 and GSM548639.

first: Chanseok

last: Shin

first: Kai

middle: H

last: Farh

first: H

last: Chiang

first: Alena

last: Shkumatava

last: Bartel


title: High resolution analysis of genomic imprinting in the embryonic and adult mouse brain AND Sex-specific imprinting in the mouse brain

first: Catherine

last: Dulac

address: BL4017 16 Divinity Ave

department: Molecular and Cellular Biology

institute: Harvard University

summary: Genomic imprinting results in the preferential expression of the paternal, or maternal allele of certain genes.  We have performed a genome-wide characterization of imprinting in the mouse embryonic and adult brain using F1 hybrid mice generated from reciprocal crosses of CASTEiJ and C57BL/6J mice. We also uncovered genes associated with sex specific parental effects in the adult mouse brain. Our study identified preferential selection of the maternally inherited X chromosome in glutamatergic neurons of the female cortex.

overall_design:
Examination of allele specific expression in the brains of reciprocal crosses of F1 hybrid mice from CASTEiJ and C57BL/6J crosses.

Processed data files (GenomicAligned, SNP_calls, TranscriptomeAligned, fRNAdbAligned) and README file linked below as supplementary files.

first: Christopher

last: Gregg