title: A human transcriptome array for high-throughput clinical studies (with a comparison to RNA-seq technology) [RNA-Seq]

status: Public on Jan 27 2011

city: Palo Alto

first: Weihong

last: Xu

address: 855 California Ave

department: Department of Biochemistry

institute: Stanford Genome Technology Center

summary: A new high-density oligonucleotide array of the human transcriptome (GG-H array) has been developed for high-throughput and cost-effective analyses in clinical studies.  This array allows comprehensive examination of gene expression and genome-wide identification of alternative splicing, as well as detection of coding SNPs and non-coding transcripts.  The GG-H array was validated using samples from multiple independent preparations of human liver and muscle, and compared with results obtained from mRNA sequencing analysis.  The GG-H array is highly reproducible in estimating gene and exon abundance, and is sensitive in detecting expression changes and alternative splicing.  This array has been implemented in a multi-center clinical program and has generated high quality, reproducible data.  When current cost, as well as sample and time requirements for sequencing are considered in the context of a required throughput of hundreds of samples per week for a clinical trial, the array provides a high-throughput and cost effective platform for clinical genomic studies.

overall_design: Examination exon/gene expression of liver and muscle in quadraplicates using both the array technology and RNA-Seq

first: Junhee

last: Seok

first: Michael

last: Mindrinos

first: Wenzhong

last: Xiao

first: Ronald

last: Davis

last: Tompkins


title: Aberrant host immune response induced by highly virulent PRRSV identified by digital gene expression tag profiling

status: Public on Dec 05 2010

city: Guangzhou

first: Yaosheng

last: Chen

state: Guangdong

address: Beisanlu,Higher education megacenter

department: School of Life Sciences

country: China

institute: Sun Yat-sen University

type: Expression profiling by high throughput sequencing

summary:
BACKGROUND: There was a large scale outbreak of the highly pathogenic porcine reproductive and respiratory syndrome (PRRS) in China and Vietnam during 2006 and 2007 that resulted in unusually high morbidity and mortality among pigs of all ages. The mechanisms underlying the molecular pathogenesis of the highly virulent PRRS virus (H-PRRSV) remains unknown. Therefore, the relationship between pulmonary gene expression profiles after H-PRRSV infection and infection pathology were analyzed in this study using high-throughput deep sequencing and histopathology.

RESULTS: H-PRRSV infection resulted in severe lung pathology. The results indicate that aberrant host innate immune responses to H-PRRSV and induction of an anti-apoptotic state could be responsible for the aggressive replication and dissemination of H-PRRSV. Prolific rapid replication of H-PRRSV could have triggered aberrant sustained expression of pro-inflammatory cytokines and chemokines leading to a markedly robust inflammatory response compounded by significant cell death and increased oxidative damage. The end result was severe tissue damage and high pathogenicity.

CONCLUSIONS: The systems analysis utilized in this study provides a comprehensive basis for better understanding the pathogenesis of H-PRRSV. Furthermore, it allows the genetic components involved in H-PRRSV resistance/susceptibility in swine populations to be identified.

overall_design:
Nine conventionally-reared, healthy 6-week-old, crossbred weaned pigs (Landrace×Yorkshire) were selected from a high-health commercial farm. All pigs were PRRSV-seronegative determined by ELISA (HerdChek PRRS 2XR; IDEXX Laboratories) and absence of PRRSV tested by RT-PCR. Pigs were randomly assigned to three groups in the experiment and raised in isolation rooms. Six pigs were inoculated with 6 ml viral suspension (4 ml intranasally and 2 ml intramuscularly) of H-PRRSV at a dose of 106.0 TCID50 ml-1 on day 0. Three negative control pigs were treated similarly with an identical volume of DMEM culture media from uninfected MARC-145 cells 1 day prior to experimental infection, and were immediately necropsied.H-PRRSV-inoculated pigs were clinically examined daily and rectal body temperatures were recorded from days -2 to 7 post infection (pi).Three infected pigs randomly chosen within each group were necropsied at each time point of 96 h pi and 168 h pi. Lung samples were collected from uninfected negative control group (C), three pigs at 96 h pi (H96), three pigs at 168 h pi (H168) and immediately frozen in liquid nitrogen for RNA isolation or fixed in 10% neutralized buffered formalin for histological processing.
Total RNA was extracted from frozen lungs using standard protocols (Trizol) and then treated with DNase to remove potential genomic DNA contamination according to the manufactures’s protocols. RNA integrity and concentration were evaluated by Agolent 2100 Bioanalyzer.For RNA library construction and deep sequencing, RNA samples were prepared as follows: for each time point of H-PRRSV-inoculated group and UNC group equal quantities of RNA isolated from three individual lungs were pooled. Approximately 6 μg of RNA representing each group were submitted to Solexa (now Illumina Inc.) for sequencing.

first: Shuqi

first: Delin

last: Mo

first: Qiwei

last: Wang

first: Jianyu

last: Jia

first: Limei

last: Qin

first: Xiangchun

last: Yu

first: Yuna

last: Niu

first: Xiao

last: Zhao

first: Xiaohong

last: Liu


title: [E-MTAB-223] ChIP-seq for FOXA1, ER and CTCF in breast cancer cell lines

status: Public on Dec 04 2010

city: Hinxton

first: ArrayExpress

last: EBI

state: Cambridgeshire

address: Wellcome Trust Genome Campus

country: United Kingdom

institute: European Bioinformatics Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
Growth cells and map of ER, FoxA1 and CTCF binding at whole genome level.

ArrayExpress Release Date: 2010-10-29

Person Roles: submitter
Person Last Name: Hurtado
Person First Name: Antoni
Person Email: toni.hurtado@cancer.org.uk
Person Affiliation: Uppsala University

overall_design:
Experimental Design: high_throughput_sequencing_design
Experimental Design: binding_site_identification_design
Experimental Factor Name: IMMUNOPRECIPITATE
Experimental Factor Name: CELL_LINE
Experimental Factor Type: immunoprecipitate
Experimental Factor Type: cell_line


title: [E-MTAB-341] Individual-nucleotide resolution CLIP using high throughput sequencing of human HeLa cells to enable precise mapping of protein-RNA interactions in intact cells

summary:
UV-crosslinking and immunoprecipitation (CLIP) combined with high-throughput sequencing was previously used to generate transcriptome-wide binding maps of several RNA-binding proteins. However, since identification of binding sites relied on the analysis of overlapping sequence clusters, distances of less than 30 nucleotides were not resolved. An additional disadvantage of CLIP is the requirement of reverse transcription to pass over residual amino acids that remain covalently attached to the RNA at the crosslink site. Primer extension assays have shown that the vast majority of cDNAs prematurely truncate immediately before the 'crosslink nucleotide'. Here, we exploited this apparent limitation to achieve single nucleotide resolution by capturing these truncated cDNAs through the introduction of a second adapter after reverse transcription via self-circularization. In order to quantify cDNA molecules that truncate at the same nucleotide, we added a random barcode to the DNA adapter. This allowed us to discriminate between unique cDNA products and PCR duplicates . Taken together, individual-nucleotide resolution CLIP (iCLIP) enables precise mapping of protein-RNA interactions in intact cells.

ArrayExpress Release Date: 2010-09-03

Publication Title: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution
Publication Author List: Konig J, Zarnack K, Rot G, Curk T, Kayikci M, Zupan B, Turner DJ, Luscombe NM, Ule J.

Person Roles: submitter
Person Last Name: Konig
Person First Name: Julian
Person Email: jkonig@mrc-lmb.cam.ac.uk
Person Phone: 0044 7531 502686
Person Address: Hills Road, CB2 0QH Cambridge, UK
Person Affiliation: MRC LMB

overall_design:
Experimental Design: in_vitro_design
Experimental Design: binding_site_identification_design
Experimental Design: high_throughput_sequencing_design
Experimental Design: transcription profiling by high throughput sequencing
Experimental Factor Name: Antibody
Quality Control Type: biological_replicate


title: [E-MTAB-214] ChiP-seq profiling of Drosophila melanogaster salivary glands to identify targets for NSL1 and MCRS2.

summary:
ChiP-seq profiling of Drosophila melanogaster salivary glands to identify targets for NSL1 and MCRS2.

ArrayExpress Release Date: 2010-04-16

Publication Title: The Nonspecific Lethal Complex Is a Transcriptional Regulator in Drosophila
Publication Author List: Raja SJ, Charapitsa I, Conrad T, Vaquerizas JM, Gebhardt P, Holz H, Kadlec J, Fraterman S, Luscombe NM, Akhtar A.

Person Roles: submitter
Person Last Name: Vaquerizas
Person First Name: Juan
Person Mid Initials: M
Person Email: jvaquerizas@ebi.ac.uk
Person Phone:
Person Address:
Person Affiliation: EBI

overall_design:
Experimental Design: individual_genetic_characteristics_design
Experimental Design: in_vivo_design
Experimental Design: binding_site_identification_design
Experimental Design: ChIP-seq
Experimental Factor Name: CHIP-ANTIBODY
Experimental Factor Type: Chip-antibody


title: [E-MTAB-197] CEU_RNASEQ60, Transcription profiling by high throughput sequencing of 60 HapMap CEU population individuals

summary:
RNA-sequencing of 60 HapMap CEU individuals

ArrayExpress Release Date: 2010-03-04

Publication Title: Transcriptome genetics using second generation sequencing in a Caucasian population
Publication Author List: Stephen B. Montgomery, Micha Sammeth, Maria Gutierrez-Arcelus, Radoslaw P. Lach, Catherine Ingle, James Nisbett, Roderic Guigo, Emmanouil T. Dermitzakis

Person Roles: submitter
Person Last Name: Montgomery
Person First Name: Stephen
Person Mid Initials: B
Person Email: stephen.montgomery@unige.ch
Person Phone: +41 (0) 22 379 5483
Person Address: 1 Rue Michel Servet, Geneva, Switzerland, 1211
Person Affiliation: University of Geneva Medical School

overall_design:
Experimental Design: individual_genetic_characteristics_design
Experimental Design: in_vitro_design
Experimental Design: high_throughput_sequencing_design
Experimental Design: co-expression_design
Experimental Factor Name: INDIVIDUAL
Experimental Factor Name: POPULATION


title: Changes in expression of small non-coding RNAs, including microRNAs, in response to stress in C. elegans

status: Public on Dec 02 2010

city: New Haven

first: Frank

middle: J

last: Slack

state: CT

address: 266 Whitney Ave

department: MCDB

country: USA

institute: Yale University

type: Non-coding RNA profiling by high throughput sequencing

summary:
To investigate the contribution of small non-coding RNAs, including microRNAs, to stress response in C. elegans, we examined their expression changes using Illumina deep-sequencing technology. Stress conditions we examined include heat shock, Pseudomonas aeruginosa (PA-14) and L1 arrest.

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: Total RNAs were purified from wild-type young adult animals that were exposed to each stress condition, and used for cDNA library preparation for small RNAs. As for the L1 arrest sample, first wild-type embryos were collected and cultured without a food source in M9 buffer for 48 hrs with rotation, and then RNAs purified from L1 animals in a developmentally arrested state were used for the library preparation. These cDNA libraries established were sequenced with Illumina Genome Analyzer II.

first: Masaomi

last: Kato


title: Identification and comparison of miRNAs involved in cotton fiber elongation between sea-island and upland cotton

status: Public on Dec 03 2010

city: Wuhan

first: Xianlong

last: Zhang

address: No.1,Shizishan Street · Hongshan District

department: National Key Laboratory of Crop Genetic Improvement

institute: Huazhong Agricultural University

summary: To identify potential miRNAs involved in fiber development and elucidate their expression differences between G. barbadense and G. hirsutum, we constructed two small RNA libraries, Gb10 and Gh10, prepared from fibers of 3-79 (G. barbadense) and TM-1 (G. hirsutum) collected at 10 days post-anthesis (DPA). We identified 28 conserved miRNA families, including 24 that exactly match known plant miRNA families in miRBase. With MIREAP and newly developed software miRsearcher, 7 candidate-novel miRNAs were found. 5 candidate-novel miRNAs were expressed in both species, 2 candidate-novel miRNAs were expressed only in one species. Moreover, 4 miRNA families showed significant expression differences between sea-island cotton and upland cotton in 10 DPA fibers.

sample_organism:
Gossypium barbadense
Gossypium hirsutum

platform_organism:
Gossypium barbadense
Gossypium hirsutum

overall_design: two examples including 3-79 and TM-1 10 DPA fibers

first: Wenxin

last: Tang

first: Peiyong

last: Jiang

first: Daojun

last: Yuan

first: Lili

last: Tu


title: PAT-ChIP-Seq: a novel tool for the epigenetic profiling of formaldehyde-fixed and paraffin-embedded (FFPE) pathology samples

city: Vienna

first: Iros

last: Barozzi

address: Borschkegasse 8a

country: Austria

institute: Medical University Vienna

summary: Epigenetic alterations in the pattern of DNA and histone modifications play a crucial role in cancer development. Analysis of patient samples, however, is hampered by technical limitations in the study of chromatin structure from pathology archives that typically consist of heavily fixed, paraffin-embedded material.

overall_design: ChIP assays (with anti-H3K4me3 and anti-H3K27me3 antibodies) were performed by using formaldehyde-fixed paraffin-embedded (FFPE) mouse spleen sections (half portion of the spleen) and comparing it to the canonical ChIP procedure applied by using isolated cells from the other portion of the same spleen.

first: Mirco

last: Fanelli

first: Stefano

last: Amatori

first: Matias

last: Soncini

first: Roberto

last: Del Zuffo

first: Gabriele

last: Bucci

first: Maria

last: Capra

first: Micaela

last: Quarto

first: Gaetano

middle: I

last: Dellino

first: Ciro

last: Mercurio

first: Myriam

last: Alcalay

first: Giuseppe

last: Viale

first: Saverio

last: Minucci

first: Pier

middle: G

last: Pelicci


title: [E-MTAB-305] ncRNA expression, including snoRNAs, across 11 tissues using polyA-neutral amplification

first: ArrayExpress

last: EBI

summary:
ncRNA expression, including snoRNAs, across 11 tissues using polyA-neutral amplification
Non-coding RNAs (ncRNAs) are an essential class of molecular species that have been difficult to monitor on high throughput platforms due to frequent lack of polyadenylation. Using a polyadenylation-neutral amplification protocol and next-generation sequencing, we explore ncRNA expression in eleven human tissues. ncRNAs 7SL, U2, 7SK, and HBII-52 are expressed at levels far exceeding mRNAs. C/D and H/ACA box snoRNAs are associated with rRNA methylation and pseudouridylation, respectively: spleen expresses both, hypothalamus expresses mainly C/D box snoRNAs, and testes show enriched expression of both H/ACA box snoRNAs and RNA telomerase TERC. Within the snoRNA 14q cluster, 14q(I-6) is expressed at much higher levels than other cluster members. More reads align to mitochondrial than nuclear tRNAs. Many lincRNAs are actively transcribed, particularly those overlapping known ncRNAs. Within the Prader-Willi syndrome loci, the snoRNA HBII-85 (group I) cluster is highly expressed in hypothalamus, greater than in other tissues and greater than group II or III. Additionally, within the disease locus we find novel transcription across a 400,000 nt span in ovaries. This genome-wide polyA-neutral expression compendium demonstrates the richness of ncRNA expression, their high expression patterns, their function-specific expression patterns, and is publicly available.

ArrayExpress Release Date: 2010-07-05

Publication Title: ncRNA expression, including snoRNAs, across 11 tissues using polyA-neutral amplification
Publication Author List: Matthew Biery,Heather Bouzek,Ronghua Chen,Stuart Jackson,Jason M. Johnson,Carol A. Rohl,Chris K. Raymond,David Haynor,Christopher D. Armour,John C. Castle

Person Roles: submitter
Person Last Name: Loewer
Person First Name: Martin
Person Mid Initials:
Person Email: martin.loewer@tron-mainz.de
Person Phone: +49 6131-720298-11
Person Address: TRON Translationale Onkologie gGmbH, Langenbeckstr. 8, D-55131 Mainz
Person Affiliation: TRON

overall_design:
Experimental Design: organism_part_comparison_design
Experimental Design: all_pairs
Experimental Design: transcription profiling by high throughput sequencing
Experimental Factor Name: ORGANISMPART
Experimental Factor Type: organism_part


title: De novo transcriptome sequencing in Anopheles funestus using Illumina RNA-seq technology

status: Public on Dec 01 2010

city: Ithaca

first: Jacob

last: Crawford

state: NY

address: 3130 Comstock Hall Cornell University

department: Entomology

institute: Cornell University

summary: We report the use of RNA-seq data to assemble transcriptional units of adult Anopheles funestus female mosquitoes. We also analyzed expression levels and protein divergence and discovered SNPs.

overall_design: Examination of full body mRNA from a single sample of 30 adult females. Center Name: Cornell-BPL. Fragments include median insert size of 103 bp,  average insert size of 250 bp with a standard deviation of 22.

middle: E

first: Wamdaogo

middle: M

last: Guelbeogo

first: Kenneth

middle: D

last: Vernick

first: N'fale

last: Sagnon

first: Brian

middle: P

last: Lazzaro


title: Genomic Profiling of HMGN1 Reveals an Association with Chromatin at Regulatory Regions

status: Public on Nov 30 2010

city: Duarte

first: Dustin

last: Schones

state: CA

address: 1500 E Duarte Rd.

institute: City of Hope

summary:
High mobility group (HMG) proteins interact with other architectural proteins to regulate chromatin structure. We performed genome-wide mapping experiments to examine the distribution of HMGN1 across the human genome.  We discovered that HMGN1 proteins are enriched at regulatory regions such as DNase I HS sites, distal transcription factor binding sites and promoters of actively transcribed genes.

YY1, the Yin Yang 1 transcription factor, is a ubiquitous transcription factor that functions either as a transcriptional activator or a repressor, depending on its interacting partner. To test the preferential localization of HMGN1 with active regulatory regions, we examined the association of transcription factor YY1 and HMGN1 in CD4+ T cells.

overall_design: Examination of the genomic profile of HMGN1 and the relationship with regulatory elements in CD4+ T cells.

first: Suresh

last: Cuddapah

first: Kairong

last: Cui

first: Tae-Young

last: Roh

first: Artem

last: Barski

first: Gang

last: Wei

first: Mark

last: Rochman

first: Michael

last: Bustin

first: Keji

last: Zhao


title: A rapid and scalable system for studying gene function in mice using conditional RNA interference

city: New York

first: Colin

middle: Dean

last: Malone

address: NYUMC, Skirball Institute, 540 1st Ave, 4-10

department: Skirball Institute - Developmental Genetics

institute: NYU Medical Center

summary:
Four libraries were analyzed to assess the level and effects of inducing the ectopic expression of a luciferase targeting miRNA in mouse embryonic fibroblasts (MEFs). Here, we find low level, leaky expression in the absence of ROSA-rtTA and doxycyclin. When expression is effectively induced, the Luciferase miRNA is expressed as the 8th most abundant species in the cells.
Keyword(s): Epigenetics

overall_design: 4 libraries were analyzed

first: Prem

middle: K

last: Premsrirut

first: Scott

middle: W

last: Lowe


title: Transcript profiling of wild-type and dcl1-5 early globular embryos

city: Cambridge

last: Nodine

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute

summary: DICER-LIKE1 (DCL1) is required for miRNA biogenesis and embryonic pattern formation. Presumably the patterning defects observed in dcl1-5 null embryos are due to the loss of miRNAs and the consequent up-regulation of their respective targets. To test which miRNA targets were up-regulated in dcl1 embryos relative to wild-type embryos, we performed genome-wide transcript profiling of wild-type and dcl1-5 early globular embryos using directional mRNA-Seq.

overall_design: For RNA isolation, pools of 30 Col-0 (wild-type) and dcl1-5 early globular embryos were hand-dissected in water, immediately transferred to 30 ul of RNAlater (Ambion), incubated at 60° C with 500 ul TRIzol Reagent (Invitrogen) for 30 minutes, and then purified according to the TRIzol Reagent protocol for RNA isolation from small quantities of tissue (Invitrogen). Two rounds of linear amplification of poly(A) RNA were performed using the Arcturus RiboAmp HS Plus kit (Molecular Devices). Strand-specific mRNA-Seq libraries were generated as previously described (Guo et al., Nature, 2010). After removing adaptor sequences, sequences were mapped to the Arabidopsis thaliana genome (TAIR9 assembly) using the Bowtie short read aligner allowing up to two mismatches within a 25 nt ‘seed’ sequence and retaining reads mapping uniquely to the genome. Since the Arcuturus RiboAmp HS Plus kit generates amplified RNAs in the antisense orientation, reads were counted as matching TAIR9 annotated genes if they overlapped the antisense strand.

first: David

last: Bartel


title: miRNA profiling of miRNAs in Hibernating Arctic Ground Squirrels

city: Shanghai

first: Wenchao

last: Hu

address: 320 Yueyang Road

department: Functional Genomics Group

institute: CAS-MPG Partner Institute for Computational Biology

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

platform_organism:
Urocitellus parryii
Mus musculus

overall_design: Refer to individual Series


title: modENCODE_White Lab: genome-wide ChIP data of GFP from EcR_WPP-4-5h on Illumina Genome Analyzer.

status: Public on Nov 24 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 GFP from EcR_WPP-4-5h 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

middle: A

last: Bild


title: modENCODE_White Lab: genome-wide ChIP data of GFP from 7T_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 7T_W3L 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


title: Understanding normal PRRSV infection in lung based on genome-wide transcriptome response identified by deep sequencing

first: Yaosheng

last: Chen

summary: Porcine reproductive and respiratory syndrome (PRRS) has been one of the most economically important diseases affecting swine industry worldwide and causes great economic losses each year. PRRS virus (PRRSV) replicates mainly in porcine alveolar macrophages (PAMs) and dendritic cells (DCs) and develops persistent infections, antibody-dependent enhancement (ADE), interstitial pneumonia and immunosuppression. But the molecular mechanisms of PRRSV infection still are poorly understood. Here we reported on the first genome-wide host transcriptional responses to normal PRRSV (N-PRRSV) infection using Solexa/Illumina’s digital gene expression (DGE) system, a tag-based high-throughput transcriptome sequencing method, and analyzed systematically the relationship between pulmonary gene expression profiles after N-PRRSV infection and infection pathology. Our results indicated that N-PRRSV appeared to utilize multiple strategies for its long surviral in infected pigs, including subverting host innate immune response, hijacking host lipid metabolism, inducing an anti-apoptotic and anti-inflammatory state as well as developing ADE. Virus-induced pro-inflammatory cytokines, chemokines, adhesion molecules and inflammatory enzymes production and inflammatory cells, antibodies, complement activation were likely to result in the development of inflammatory responses during N-PRRSV infection processing. N-PRRSV-induced immunosuppression might be mediated by apoptosis of infected cells, which caused depletion of immune cells and induced an anti-inflammatory cytokine response in which they were unable to eradicate the primary infection or developed secondary infection. Our systems analysis will benefit for better understanding the molecular pathogenesis of N-PRRSV infection, developing novel antiviral therapies and identifying genetic components for swine resistance/susceptibility to PRRS.

overall_design:
Nine conventionally-reared, healthy 6-week-old, crossbred weaned pigs (Landrace×Yorkshire) were selected from a high-health commercial farm.All pigs were PRRSV-seronegative determined by ELISA (HerdChek PRRS 2XR; IDEXX Laboratories) and absence of PRRSV tested by RT-PCR. Pigs were randomly assigned to three groups in the experiment and raised in isolation rooms. Six pigs were inoculated with 6 ml viral suspension (4 ml intranasally and 2 ml intramuscularly) of North American type PRRSV (N-PRRSV, isolated from China) at a dose of 106.0 TCID50 ml-1 on day 0. Three negative control pigs were treated similarly with an identical volume of DMEM culture media from uninfected MARC-145 cells 1 day prior to experimental infection, and were immediately necropsied.N-PRRSV-inoculated pigs were clinically examined daily and rectal body temperatures were recorded from days -2 to 7 post infection (pi).Three infected pigs randomly chosen within each group were necropsied at each time point of 96 h pi and 168 h pi. Lung samples were collected from uninfected negative control group (C), three pigs at 96 h pi (N96), three pigs at 168 h pi (N168) and immediately frozen in liquid nitrogen for RNA isolation or fixed in 10% neutralized buffered formalin for histological processing.
Total RNA was extracted from frozen lungs using standard protocols (Trizol) and then treated with DNase to remove potential genomic DNA contamination according to the manufactures’s protocols. RNA integrity and concentration were evaluated by Agolent 2100 Bioanalyzer.For RNA library construction and deep sequencing, RNA samples were prepared as follows: for each time point of H-PRRSV-inoculated group and UNC group equal quantities of RNA isolated from three individual lungs were pooled. Approximately 6 μg of RNA representing each group were submitted to Solexa (now Illumina Inc.) for sequencing.

first: Shuqi

last: Xiao

first: Jianyu

last: Jia

first: Qiwei

last: Wang

first: Limei

last: Qin

first: Xiao

first: Dolin

last: Mo

first: Xiaohong

last: Liu


title: miRNA profiling by Illumina sequencing technology

summary: miRNAs are 19-25 nucleotides long small RNAs now well-known for their regulatory roles in the development and diseases through post-transcriptional and translational controls in a wide range of species. Mammalian hibernation is a physiological process involving dramatic metabolic suppression and cellular reorganization, during which miRNAs may play an important role. We systematically analyzed the miRNAs in the liver of an extreme hibernating species, arctic ground squirrels (Spermophilus parryii), during two stages of hibernation compared to non-hibernating animals by massively parallel Illumina sequencing technology. We identified more than 200 ground squirrel miRNAs including novel miRNAs specific to ground squirrel and a fast-evolving miRNA cluster that also showed significant differential expression during hibernation. Integrating with Agilent miRNA microarray and Real-time PCR results, we identified that mir-211, mir-378, mir-184, mir-200a, and mir-320 were significantly under-expressed during hibernation, whereas mir-144, mir-486, mir-451, mir-142-5p, and mir-1 were over-expressed. Analyses of the their target genes suggested that these miRNAs could play an important role to suppress tumor progression and cell growth during hibernation.

overall_design: Investigation of microRNA changes in arctic ground squirrel livers during Early Arousal(EA), Late Topor(LT), and Post-Reproduction(PR) stages.

first: Yuting

first: Haifang

first: Chunxuan

last: Shao

first: Minghua

last: Lu

first: Zheng

last: Yan

first: Philipp

last: Khaitovich

first: Wei

first: Brian

last: Barnes

first: Jun


title: modENCODE_White Lab: genome-wide ChIP data of Trem from Adult-Female on Illumina Genome Analyzer.

first: Kevin

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 Trem from Adult-Female 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

first: Nicolas

first: Nicholas


title: modENCODE_White Lab: genome-wide ChIP data of HP1-Abcam from 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 HP1-Abcam from E16-24h 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


title: modENCODE_White Lab: genome-wide ChIP data of KW3-D-D2 from E0-8h_D 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 KW3-D-D2 from E0-8h_D 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 KW3-D-D2 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


title: modENCODE_White Lab: genome-wide ChIP data of HP1-Covance from 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 HP1-Covance from E16-24h 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


title: modENCODE_White Lab: genome-wide ChIP data of KW4-Hr39-D1 from 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 KW4-Hr39-D1 from E16-24h 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


title: Bcl6 and NFkB cistromes mediate opposing reulation of the innate immune response

city: La Jolla

first: Ruth

middle: T

last: Yu

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

summary:
Here, using ChIP-seq, we define the NF-κB cistrome which is comprised of 31,070 cis-acting binding sites responsive to LPS-induced signaling.  In addition, we demonstrate that the transcriptional repressor B-cell lymphoma 6 (Bcl-6) regulates nearly a third of the Tlr4-regulated transcriptome and that 90% of the Bcl-6 cistrome is collapsed following Tlr4 activation.  Bcl-6 deficient macrophages are acutely hypersensitive to lipopolysaccharide (LPS) and, using comparative ChIP-seq analyses, we find that the Bcl-6 and NF-κB cistromes intersect, within nucleosomal distance, at nearly half of Bcl-6 binding sites in stimulated macrophages to promote opposing epigenetic modifications of the local chromatin.  These results reveal a genomic strategy for controlling the innate immune response in which repressive and inductive cistromes establish a dynamic balance between macrophage quiescence and activation via epigenetically marked cis-regulatory elements.

keywords: Genome-wide location analysis

overall_design: Identification of BCL6 and NFkB binding sites in unstimulated and LPS-stimulated primary bone-marrow derived macrophages.

first: Grant

last: Barish

first: Ronald

last: Evans


title: modENCODE_White Lab: genome-wide ChIP data of KW3-Trl-D2 from E8-16h on Illumina Genome Analyzer.

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 KW3-Trl-D2 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

last: Negre


title: High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells

status: Public on Nov 18 2010

city: Chapel Hill

first: Terry

last: Furey

state: NC

address: 5022 Genetic Medicine Building, CB#7264

department: Genetics

institute: UNC-Chapel Hill

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

This SuperSeries is composed of the SubSeries listed below.

relation:
SuperSeries of: GSE25344
SuperSeries of: GSE25416


title: [E-MTAB-308] Zebrafish gene 3 prime end pull down for genome annotation

first: ArrayExpress

last: EBI

summary:
As part of the zebrafish genome annotation project the 3 prime ends of genes were pulled down on polyT beads and sequenced on the Illumina Genome Analyzer to identify alternative 3 prime ends in a range of tissues and developmental stages.
Total RNA from a range of developmental stages and adult tissues were chemically fragmented, pulled down on polyT magnetic beads and double stranded cDNA was synthesized. The cDNA was BpmI digested to release from the beads and to leave a 6 T base tail. Illumina sequencing libraries were made followed by 76 base paired-end sequencing.

ArrayExpress Release Date: 2010-10-14

Person Roles: submitter
Person Last Name: Collins
Person First Name: John
Person Mid Initials: E
Person Email: jec@sanger.ac.uk
Person Phone: 01233 834244
Person Address: Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1HH, United Kingdom
Person Affiliation: Wellcome Trust Sanger Institute

overall_design:
Experimental Design: development_or_differentiation_design
AEExperimentType: transcription profiling by high throughput sequencing
Experimental Factor Name: AGE
Experimental Factor Name: ORGANISM_PART
Experimental Factor Name: DEVELOPMENTAL_STAGE
Experimental Factor Name: SEX
Experimental Factor Type: age
Experimental Factor Type: organism_part
Experimental Factor Type: developmental_stage
Experimental Factor Type: sex


title: High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells (ChIP-seq)

summary:
Using DNaseI hypersensitivity (HS) assays (Dnase-seq), high resolution DNaseI digestion profiles were generated genome-wide in diverse human cell types.  We showed that within general regions of DNaseI HS that are known to identify locations of gene regulatory elements, DNaseI digestion patterns allowed us to identify locations of individual transcription factor binding sites that protected against the bound DNA against digestion. To measure the accuracy of these footprints, we also generated ChIP-seq data for the CTCF DNA binding factor in the same cell growths.  We found that DNaseI footprints containing the CTCF canonical binding motif show significant ChIP-seq signal while CTCF binding motifs not in footprints show almost no signal providing one measure of valdation of the DNaseI footprints.

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: Five cell lines representing cervica carcinoma, chronic myeloid leukemia, embryonic stem cells, epidermal keratinocytes, and umbilical vein endothelial cells were analyzed using ChIP-seq.

first: Vishwanath

middle: R

last: Iyer

first: Terrence

middle: S

first: Gregory

last: Crawford


title: High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells (Dnase-seq)

overall_design: Six cell lines representing cervica carcinoma, chronic myeloid leukemia, human embryonic stem cells, lymphoblastoid cells, human epidermal keratinocytes and umbilical vein endothelial cells were analyzed using Dnase-seq.


title: Mediation of CTCF transcriptional insulation by DEAD-box RNA-binding protein p68 and steroid receptor RNA activator SRA

status: Public on Nov 16 2010

city: Bethesda

last: Brick

state: MD

address: 5/205 Memorial Drive

department: GBB

institute: NIDDK

summary: CCCTC-binding factor (CTCF) is a DNA-binding protein that plays important roles in chromatin organization, though the mechanism by which CTCF carries out these functions is not fully understood. Recent studies show that CTCF recruits the cohesin complex to insulator sites and that cohesin is required for insulator activity. Here we have shown that the DEAD box RNA helicase p68 (DDX5) and its associated noncoding RNA, steroid receptor RNA activator (SRA), form a complex with CTCF that is essential for insulator  function. p68 was detected at CTCF sites in the IGF2/H19 imprinted control region (ICR) as well as other genomic CTCF sites. In vivo depletion of SRA or p68 reduced CTCF-mediated insulator activity at the IGF2/H19 ICR, increased levels of IGF2 expression, and increased interactions between the endodermal enhancer and IGF2 promoter. p68/SRA also interacts with members of the cohesin complex. Depletion of either p68 or SRA does not affect CTCF binding to its genomic sites, but it does reduce cohesin binding. The results suggest that p68/SRA stabilizes the interaction of cohesin with CTCF, by binding to both, and is required for proper insulator function.

overall_design: Identification of p68-binding sites in Hela cells using ChIP-Seq.

first: Hongjie

last: Yao

first: Yvonne

last: Evrard

first: Tiaojiang

last: Xiao

first: Rafael

last: Camerini-Otero

first: Gary

last: Felsenfeld


title: Histone methylation and transcription factor binding during intestinal cell differentation

status: Public on Nov 17 2010

city: Piscataway

first: Michael

last: Verzi

state: NJ

address: 145 Bevier Road

institute: Rutgers, the State University of New Jersey

summary: Cell differentiation requires epigenetic modulation of tissue-specific genes and activities of master transcriptional regulators, which are recognized for their dominant control over cellular programs. Using novel epigenomic methods, we characterized enhancer elements specifically modified in differentiating intestinal epithelial cells and found enrichment of transcription factor-binding motifs corresponding to CDX2, a master regulator of the intestine. Directed investigation revealed surprising lability in CDX2 occupancy of the genome, with redistribution from hundreds of sites occupied only in progenitors to thousands of new sites in mature cells. Knockout mice confirmed distinct Cdx2 requirements in dividing and differentiated adult intestinal cells, including responsibility for the active enhancer configuration associated with maturity. Dynamic CDX2 occupancy corresponds with condition-specific gene expression and, importantly, to differential co-occupancy with other tissue-restricted transcription factors: HNF4A in mature cells and GATA6 in progenitors. These results reveal dynamic, context-specific functions and mechanisms of a master transcription factor within a cell lineage.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: H3K4me2, CDX2, GATA6, and HNF4A ChIP-seq patterns were mapped in proliferating and 26 day post-confluent (differentatied) Caco-2 intestinal cell lines and compared to published expression data or newly generated Cdx2 knockout mouse intestine expression data

first: Ramesh

last: Shivdasani

first: X

last: Liu

first: Hyunjin

last: Shin


title: Accurate inference of transcription factor binding  from DNA sequence and chromatin accessibility data

status: Public on Nov 15 2010

first: Jacob

middle: F

last: Degner

department: Human Genetics

summary: Accurate functional annotation of regulatory elements is essential for understanding global gene regulation. Here, we report a genome-wide map of 827,000 transcription factor binding sites in human lymphoblastoid cell lines, which is comprised of sites correspond-ing to 239 position weight matrices of known transcription factor binding motifs, and 49 novel sequence motifs. To generate this map, we developed a probabilistic framework that integrates cell- or tissue-speciﬁc experimental data such as histone modiﬁcations and DNa-seI cleavage patterns with genomic information such as gene annotation and evolutionary conservation. Comparison to empirical ChIP-seq data suggests that our method is highly accurate yet has the advantage of targeting many factors in a single assay. We anticipate that this approach will be a valuable tool for genome-wide studies of gene regulation in a wide variety of cell-types or tissues under diverse conditions.

overall_design: DNaseI-Seq on two YRI Hapmap cell lines. Each individual sequenced on 8 lanes of the Illumina Genome Analyzer II

first: Roger

last: Pique-Regi

first: Athma

last: Pai

first: Daniel

last: Gaffney

first: Yoav

last: Gilad

first: Jonathan

last: Pritchard


title: Genome-wide binding of the orphan nuclear receptor TR4 suggests its general role in fundamental biological processes

first: Philip

last: Cayting

address: 1501 S California Ave

institute: Stanford University

summary:
The orphan nuclear receptor TR4 (human testicular receptor 4 or NR2C2) plays a pivotal role in a variety of biological and metabolic processes. With no known ligand and few known target genes, the mode of TR4 function was unclear. We report the first genome-wide identification and characterization of TR4 in vivo binding. Using chromatin immunoprecipitation followed by high throughput sequencing (ChIP-seq), we identified TR4 binding sites in 4 different human cell types and found that the majority of target genes were shared among different cells. TR4 target genes are involved in fundamental biological processes such as RNA metabolism and protein translation. In addition, we found that a subset of TR4 target genes exerts cell-type specific functions.  Analysis of the TR4 binding sites revealed that less than 30% of the peaks from any of the cell types contained the DR1 motif previously derived from in vitro studies, suggesting that TR4 may be recruited to the genome via interaction with other proteins.  A bioinformatics analysis of the TR4 binding sites predicted a cis regulatory module involving TR4 and ETS transcription factors. To test this prediction, we performed ChIP-seq for the ETS factor ELK4 and found that 30% of TR4 binding sites were also bound by ELK4.  Motif analysis of the sites bound by both factors revealed a lack of the DR1 element, suggesting that TR4 binding at a subset of sites is facilitated through the ETS transcription factor ELK4. Further studies will be required to investigate the functional interdependence of these two factors.

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: 8 total ChIP-seq datasets; four TR4 and datasets done in duplicate from 4 different cell lines; ELK4 (Sap1a) duplicate dataset done  from HeLa cells; 1 ELK1 replicate in HeLa cells, 2 individual replicates for histone mod datasets  from K562 cells

first: Henriette

last: O'Geen

first: Peggy

last: Farnham


title: modENCODE_White Lab: genome-wide ChIP data of GFP from 15T_8-16_NW on Illumina Genome Analyzer.

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 GFP from 15T_8-16_NW 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

first: Nicolas

last: Negre

first: Nicholas

last: Bild


title: ZNF274 colocalizes with the histone methyltransferase SETDB1 at ZNF 3' ends.

summary:
Only a small percentage of human transcription factors (e.g. those associated with a specific differentiation program) are expressed in a given cell type. Thus, cell fate is mainly determined by cell type-specific silencing of transcription factors that drive different cellular lineages.  Several histone modifications have been associated with gene silencing, including H3K27me3 and H3K9me3. We have previously shown that the two largest classes of mammalian transcription factors are marked by distinct histone modifications; homeobox genes are marked by H3K27me3 and zinc finger genes are marked by H3K9me3. Several histone methyltransferases (e.g. G9a and SETDB1) may be involved in mediating the H3K9me3 silencing mark. We have used ChIP-chip (GSE24480) and ChIP-seq to demonstrate that SETDB1, but not G9a, is associated with regions of the genome enriched for H3K9me3. A current model is that SETDB1 is recruited to specific genomic locations via interaction with the corepressor TRIM28 (KAP1), which is in turn recruited to the genome via interaction with zinc finger transcription factors that contain a Kruppel-associated box (KRAB) domain. However, specific KRAB-ZNFs that recruit TRIM28 (KAP1) and SETDB1 to the genome have not been identified. We now show that ZNF274 (a KRAB-ZNF that contains 5 C2H2 zinc finger domains), can interact with KAP1 in vitro and, using ChIP-seq, we show that ZNF274 binding sites co-localize with SETDB1, KAP1, and H3K9me3 at the 3’ ends of zinc finger genes. Knockdown of ZNF274 with siRNAs reduced the levels of KAP1 and SETDB1 recruitment to the binding sites. These studies provide the first identification of a KRAB domain-containing ZNFs that is involved in recruitment of the KAP1 and SETDB1 to the human genome.

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: 7 total ChIP-seq datasets; 4 ZNF274 datasets done in duplicate from 4 different cell lines; 1 KAP1 duplicate dataset done in duplicate from K562 cells; 1 SetDB1 duplicate dataset from K562 cells; 1 H3K9me3 duplicate dataset from K562 cells

first: Seth

last: Frietze


title: BI Human Reference Epigenome Mapping Project: Characterization of DNA methylation by RRBS in human subject

status: Public on Nov 11 2010

first: BROAD

last: INSTITUTE

institute: Broad Institute

type: Methylation profiling by high throughput sequencing

summary:
Characterization of the reference epigenome in humans in a diverse panel of ES cells, tissue stem cells, reprogrammed stem cells, primary cells and tissues

****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

overall_design:
BI Human Reference Epigenome Mapping Project - samples and experiments will continue to be added to this study over the course of the project.

EDACC Genboree Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSTUDY%2FEDACC.2296

first: Bradley

last: Bernstein

first: Alex

last: Meissner


title: BI Human Reference Epigenome Mapping Project: Characterization of DNA methylation by RRBS

summary:
Characterization of the reference epigenome in humans in a diverse panel of ES cells, tissue stem cells, reprogrammed stem cells, primary cells and tissues.

****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

overall_design:
BI Human Reference Epigenome Mapping Project - samples and experiments will continue to be added to this study over the course of the project.

EDACC Genboree Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSTUDY%2FEDACC.1899


title: Identification of miRNAs and their target genes in developing seeds of soybean by deep sequencing

city: beijing

first: Jinsong

last: Zhang

address: No.1 West Beichen Road,Chaoyang District

institute: IGDB

summary: In our study, small RNA library and degradome library were constructed from developing soybean seeds for deep sequencing. We identified 26 new miRNAs in soybean by bioinformatic analysis, and further confirmed their expression by stem-loop RT-PCR. The miRNA star sequences of 38 known miRNAs and 8 new miRNAs were also discovered, providing additional evidence for the existence of miRNAs. Through degradome sequencing, 145 and 25 genes were identified as targets of annotated miRNAs and new miRNAs, respectively. Many identified miRNA targets may perform functions in soybean seed development by GO analysis. Additionally, soybean homolog of Arabidopsis SUPPRESSOR OF GENE SLIENCING 3(AtSGS3) was detected as target of the new identified miRNA Soy_25, suggesting presence of feedback control of miRNA biogenesis

overall_design:
sample 1: Examination of small RNA in soybean seed
sample 2: identification of miRNA targets in soybean seed

first: Qing-Xin

last: Song

first: Jin-Song


title: modENCODE_White Lab: genome-wide ChIP data of GFP from ECR-WPP+90 on Illumina Genome Analyzer.

status: Public on Nov 10 2010

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 ECR-WPP+90 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.


title: modENCODE_White Lab: genome-wide ChIP data of GFP from 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 E16-24h 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


title: modENCODE_White Lab: genome-wide ChIP data of GFP from ECR-WPP+12 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 ECR-WPP+12 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


title: modENCODE_White Lab: genome-wide ChIP data of GFP from 5T-0-6 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 5T-0-6 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


title: BI Human Reference Epigenome Mapping Project: Characterization of DNA methylation by RRBS in HUES lines

overall_design:
BI Human Reference Epigenome Mapping Project - samples and experiments will continue to be added to this study over the course of the project.

EDACC Genboree Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSTUDY%2FEDACC.4057


title: Synthetic antagonist of a histone reader reveals and targets genes essential for inflammation

first: Uwe

last: Schaefer

address: 1230 York Ave.

institute: Rockefeller University

summary: Post-translational modifications of histones determines cell lineage- or signal-specific gene expression.  Depending on the type and combination of modifications, histones bind to functionally distinct effector proteins ('readers') that control gene activation or silencing. The current pharmacological modulation of the epigenome aims to control gene expression by regulation of the enzymes that catalyze post-translational histone modifications. Here we present a novel pharmacological approach that targets gene expression by interfering with the function of  histone  ?readers?. We describe the impact of a synthetic compound that selectively occupies the acetylated histone-binding pocket of the Bromodomain and Extra Terminal domain (BET) family of proteins and prevents their interaction with acetylated histones. The bromodomain blocking compound suppresses the expression of a specific subset of key inflammatory genes in activated macrophages and confers protection against LPS-induced septic shock in vivo.  Our findings suggest that small molecules specifically targeting histone 'readers' can serve as a new generation of drugs to treat immune diseases.

overall_design: Microarray, ChIP-qPCR and ChIP-seq examination of control, 1H LPS stimulated bone-marrow-derived macrophages in the presence/absence of acetylated histone mimic in mouse.

first: Scott

last: Dewell


title: Analysis and design of RNA sequencing experiments for identifying mRNA isoform regulation

status: Public on Nov 07 2010

city: Gainesville

first: Eric

last: Wang

state: FL

address: 2033 Mowry Rd

institute: University of Florida

summary: Through alternative splicing, most human genes express multiple isoforms that may have distinct or even antagonistic functions. To infer isoform regulation based on data from high-throughput sequencing of cDNA fragments (RNA-Seq), we have developed MISO, a computational model that estimates the expression level of alternatively spliced exons and mRNA isoforms and provides intuitive measures of conﬁdence in these estimates. Incorporation of the length distribution of inserted cDNA fragments in paired-end RNA-Seq analysis in MISO enables dramatic improvements in estimation of alternative splicing levels relative to previous methods. We show that one lane of paired-end RNA-Seq data can provide far more information about splicing than two lanes of single-end data, depending critically on properties of the distribution of cDNA fragment lengths in the sequenced library. MISO also leads to an intuitive method to detect diﬀerentially regulated exons  or isoforms. Application of this method implicates the RNA splicing factor hnRNP H in regulation of alternative cleavage and polyadenylation, a role that is supported by UV  crosslinking/immunoprecipitation/high-throughput sequencing (CLIP-Seq) analysis. Together, our results provide a probabilistic framework for RNA-Seq analysis, derive functional insights into pre-mRNA processing, and yield guidelines for the optimal design of RNA-Seq experiments for studies of gene and isoform expression.

overall_design:
CLIPseq of hnRNP H in HEK 293T cells.
RNAseq of polyA+ RNA from C2C12 mouse myoblasts stably expressing an empty vector or a vector containing an shRNA against CUGBP1. Libraries of two different insert lengths were created and examined.

first: Yarden

last: Katz

first: Edoardo

last: Airoldi

first: Chris

last: Burge


title: FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing.

city: Santa Cruz

first: Andrew

middle: V

last: Uzilov

address: 1156 High St, MS SOE3

institute: University of California, Santa Cruz

summary: To accelerate previous RNA structure probing approaches, which focus on analyzing one RNA sequence at a time, we have developed FragSeq, a high-throughput RNA structure probing method that uses high-throughput RNA sequencing to identify single-stranded RNA (ssRNA) regions from fragments generated by nuclease P1, which is specific for single-stranded nucleic acids. In the accompanying study, we show that we can accurately and simultaneously map ssRNA regions in multiple non-coding RNAs with known structure in experiments probing the entire mouse nuclear transcriptome. We carried out probing in two cell types to assess reproducibility. We also identified and experimentally validated structured regions in ncRNAs never previously probed.

overall_design: We examined mouse nuclear RNA from two cell types: undifferentiated embryonic stem cells (UNDIFF) and cells differentiated into neural precursors (D5NP). For each cell type, nuclear RNA was purified and deproteinized, denatured, and refolded in vitro, from which we prepared three barcoded samples: "nuclease" (RNA partially digested with P1 ssRNA-specific nuclease, yielding 5'-PO4/3'-OH end chemistry at each cleavage site), "control" (control for "nuclease" sample to idenfity endogenous 5'-PO4/3'-OH), and "PNK" (same as "control" but followed by a polynucleotide kinase treatment to convert 5'-OH/3'-cyclic-phosphate ends to clonable 5'-PO4/3'-OH ends). Resulting RNA fragments were cloned using the SOLiD Small RNA Expression Kit (SREK) protocol, which ligates linkers only to 5'-PO4/3'-OH containing RNA, enriching for clones of products resulting from P1 cleavage in "nuclease" sample and selecting against random degradation. Two cell types, three treatments each, thus resulted in six barcoded samples total (barcodes 01, 02, 04, 05, 07, 08). Four other barcoded samples were prepared for separate experiments not used in our study (barcodes 03, 06, 09, 10), so their preparation is not described here. The total run of ten barcodes was done on the ABI SOLiD3 platform and a custom algorithm (FragSeq v0.0.1) was used to compute "cutting scores" (as described in our paper) that show ssRNA regions in hundreds of ncRNAs.

first: Jason

last: Underwood

first: Sol

last: Katzman

first: Courtney

last: Onodera

first: Jacob

last: Mainzer

first: David

middle: H

last: Mathews

first: Todd

last: Lowe

first: Sofie

last: Salama

last: Haussler


title: Distribution of macroH2A1 nucleosomes in mouse liver chromatin

city: Philadelphia

first: John

last: Pehrson

state: PA

address: 3800 Spruce Street

institute: University of Pennsylvania

summary: We produced a genome-wide map of the distribution of macroH2A1 histone variants in mouse liver chromatin using high-throughput sequencing of DNA from macroH2A1 nucleosomes. Although macroH2A1 nucleosomes are widely distributed across the genome, their local concentration varies over a range of 100-fold or more. The transcribed regions of most active genes are depleted of macroH2A1, with many showing depletion of 3-fold or more. The inactive X chromosome appears to have relatively uniform macroH2A1 enrichment that averages approximately 3.9-fold, but most genes that are known to escape from X inactivation do not show this enrichment. We used macroH2A1 depletion to identify additional genes that escape X inactivation, but overall, our map supports the idea that relatively few genes escape in the mouse. The map also helped identify genes that appear to be direct targets of macroH2A1-mediated repression.

overall_design:
MacroH2A1 nucleosomes were purified from female mouse liver chromatin by thiol-affinity chromatography (Mol. Cell Biol. 26, 4410 (2006)) and their distribution was compared to that of the bulk nucleosomes used as the starting material for the purification. Nucleosomal DNA from two independent preparations was pooled and mononucleosomal DNA was prepared from both macroH2A1 and starting material nucleosomes. Each preparation used 8 to 10 livers from 8 to 10 week old female mice.

For the relative macroH2A1 content file (see supplementary file), we used tools in the rna-seq workflow of Partek Genomics Suite (version 6.5b, 6.09.0806, Partek Inc.) to calculate the relative macroH2A1 content of individual genes. This program counts and normalizes hits in predefined regions specified in a refFlat file. The gene list was the Mouse build 8 version of refFlat.txt obtained from the UCSC Genome site. All exon information was stripped from the refFlat.txt file, which left only the start and stop sites for the genes. Normalized RPKM (reads per kilobase per million reads) values were compared to calculate fold change and FDR-adjusted p-values for each transcript.

first: Lakshmi

middle: N

last: Changolkar

first: Geetika

last: Singh

first: Kairong

last: Cui

first: Joel

middle: B

last: Berletch

first: Keji

last: Zhao

first: Christine

last: Disteche


title: smRNAs in wildtype and RDR6-15 knockout Arabidopsis thaliana Col-0 leaf

status: Public on Nov 22 2010

first: Thomas

middle: James

last: Hardcastle

address: Downing Street

department: Plant Sciences

institute: University of Cambridge

summary: This set consists of small RNAs sequenced from two replicates of wildtype and two replicates of RDR6-15 knockout Arabidopsis thaliana Col-0 leaf samples. RDR6 is required for the production of tasRNAs (trans-acting small RNAS) and so tags associated with the tasRNA loci should be severely down-regulated or absent in the knockout compared to wildtype. The set can thus be used as containing known true positives for testing differential expression detection methods.

overall_design: Examination of smRNA in 2 replicates wildtype and 2 replicates RDR6-15 knockout

middle: J

first: Nataliya

last: Elina


title: Structural annotation of equine protein-coding genes determined by mRNA sequencing

city: Fort Collins

first: Stephen

last: Coleman

state: CO

address: 1682 Campus Delivery

department: MIP

institute: Colorado State University

summary: The horse, like a majority of animal species, has a limited amount of species-specific expressed sequence data available in public databases.  As a result, structural models for a majority of genes defined in the equine genome are predictions based on ab initio sequence analysis or the projection of gene structures from other mammalian species.  The current study used Illumina-based sequencing of messenger RNA (RNA-seq) to help refine structural annotation of equine protein-coding genes and for a preliminary assessment of gene expression patterns.  Sequencing of mRNA from eight equine tissues generated 293,758,105 thirty five-base sequence tags, equaling 10.28 giga-basepairs of total sequence data.  The tag alignments represent approximately 208X coverage of the equine mRNA transcriptome and confirmed transcriptional activity for roughly 90% of the protein-coding gene structures predicted by Ensembl and NCBI.  Tag coverage was sufficient to define structural annotation for 11,356 genes, while also identifying an additional 456 transcripts with exon/intron features that are not listed by either Ensembl or NCBI.  Genomic locus data and intervals for the protein-coding genes predicted by the Ensembl and NCBI annotation pipelines were combined with 75,116 RNA-seq derived transcriptional units to generate a consensus equine protein-coding gene set of 20,302 defined loci.  Gene ontology annotation was used to compare the functional and structural categories of genes expressed in either a tissue-restricted pattern or broadly across all tissue samples.

overall_design: Examination of 8 equine RNA samples representing 6 distinct tissues

first: James

last: MacLeod


title: Identification of Neuronal RNA Targets of TDP-43-Containing Ribonucleoprotein Complexes

status: Public on Nov 04 2010

city: Worcester

first: Alper

last: Kucukural

address: 364 Plantation Street

department: Program in Molecular Medicine

institute: UMass Medical School

summary: We identify the RNA targets of TAR DNA-binding protein 43 (TDP-43) from cortical neurons by RNA immunoprecipitation followed by deep sequencing (RIP-seq). We identify 4352 highly enriched RNA targets of TDP-43. We determined that the canonical TDP-43 binding site (TG)n was 55.1-fold enriched in our TDP-43 library. Moreover, our analysis shows there is often an adenine in the middle of the motif, (TG)nTA(TG)m. TDP-43 RNA targets are particularly enriched for Gene Ontology terms related to RNA metabolism, neuronal development, and synaptic function.

overall_design:
Examination of TDP-43 RNA targets in rat cortical neurons by RIP-seq.

Chantelle F. Sephton isolated the TDP-43:RNA complexes and generated the cDNA library for deep sequencing.
Email: chantelle.sephton@utsouthwestern.edu
Phone: 214-648-4119
Fax: 214-648-1801
ULR: http://www8.utsouthwestern.edu/utsw/cda/dept120915/files/151135.html
Organization name: University of Texas Southwestern Medical Center at Dallas
Department: Neuroscience
Lab: Gang Yu lab
Street: 6000 Harry Hines Blvd.
City: Dallas
State: Texas
ZIP: 75390
Country: USA

first: Chantelle

last: Sephton

first: Can

last: Cenik

first: Eric

last: Dammer

first: Basar

first: Yu-Hong

last: Han

first: Colleen

middle: M

last: Dewey

first: Frederick

last: Roth

first: Joachim

last: Herz

first: Junmin

last: Peng

first: Melissa

last: Moore

first: Gang

last: Yu


title: Genomic maps of homotypic H2Av, heterotypic H2Av, input and 80mM salt soluble chromatin from Drosophila S2 cells

status: Public on Nov 01 2010

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

summary: Nucleosomes that contain the histone variant H2A.Z are enriched around transcriptional start sites in many organisms. A single octameric nucleosome can contain two H2A.Z histones (homotypic) or one H2A.Z and one canonical H2A (heterotype). We generated high-resolution maps of homotypic and heterotypic Drosophila H2A.Z (H2Av) nucleosomes. Although homotypic and heterotypic H2Av nucleosomes map throughout most of the genome, homotypic nucleosomes are enriched and heterotypic nucleosomes are depleted downstream of active promoters and intron/exon boundaries. The distribution of homotypic H2A.Z nucleosomes resembles that of salt-soluble nucleosomes and shows evidence of displacement during transcriptional elongation. Homotypic nucleosomes are also depleted downstream of paused polymerases, where salt-soluble nucleosomes are conspicuously depleted. Our results suggest a model whereby H2A.Z enrichment patterns result from different structural interactions within the core of heterotypic and homotypic nucleosomes following disruption during transcriptional elongation.

overall_design: We analyzed two replicates for input, heterotypic and homotypic purifications. We sequenced one library for each of the single H2Av pulldown and 80mM salt soluble samples.

first: Christopher

last: Weber

middle: G

first: Steven


title: Investigation of the microRNAs in safflower seed, leaf and petal by high-throughput sequencing

status: Public on Nov 06 2010

city: Qingdao

first: Naihao

last: Ye

address: Yellow Sea Fisheries Research Institute (YSFRI), Chinese Academy of Fishery Sciences, Qingdao, 266071, China

summary: We report that there are at least 236 known miRNAs expressed in safflower, of which 100 miRNAs with relatively high expression level exhibited evolutionary conservation across multiple plants. Comparison of their expression patterns among different tissues shows that a total of 116, 133 and 128 miRNAs are significantly differentially expressed between safflower seed/leaf, seed/petal and leaf/petal. Meanwhile, interestingly, the majority of the most significantly differentially expressed miRNAs between tissues are tissue-specific miRNAs. In addition, 15 putative novel miRNAs have been identified in safflower. The small RNA transcriptomes obtained in this study provide a basis for further investigation of the physiological roles of identified miRNAs in safflower.

overall_design: Investigate the small RNA transcriptomes in 3 tissues

first: Haiyan

last: Li

first: Yuanyuan

last: Dong


title: Genome-wide target discovery of transcripton factor E2F4 by ChIP-seq

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

summary: The transcription factor E2F4 is a member of the E2F family of regulators which has critical roles in cell cycle control and differentiation. In order to fully understand the physiological roles of E2F4 and the regulatory networks it mediates, and to reveal its relationships with other members of the E2F family, it is essential to comprehensively identify E2F4 target sites throughout the genome. Here, we investigated genome-wide E2F4 targets in human lymphoblastoid cells using the recently developed unbiased target discovery technique of ChIP sequencing.

overall_design: We sequecned E2F4 ChIP and corresponding Input

first: Bum-Kyu

last: Lee

first: Akshay

last: Bhinge

first: Vishwanath


title: Expression profile of third instar larval fat body and midgut tissues

status: Public on Nov 02 2010

first: Terry

middle: L.

last: Orr-Weaver

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: We use mRNA-seq to transcriptionally profile larval fat body and midgut tissues from Drosophila third instar larvae. These data provide insights into tissue physiology and can be used to identify tissue specific transcripts.

overall_design: Fat bodies from wandering third instar larvae were dissected from ~50 male larvae and gonads were removed to eliminate contaminating transctips from the gonads. Larval midguts were dissected from ~50 wandering third instar larvae. Larval tissues were removed to Graces unsupplemented medium on ice prior to RNA extraction with TRIzol reagent. mRNA-seq samples were prepared from 5ug of total RNA and subject to Illumina based sequencing.

first: Jared

last: Nordman

first: Sharon

first: Thomas

last: Eng

first: David

last: MacAlpine

middle: L


title: Wide-ranging fucntions of E2F4 in transcriptional activation and repression revealed by genome-wide analysis

summary:
The transcription factor E2F4 is a member of the E2F family of regulators which has critical roles in cell cycle control and differentiation. We investigated the genome-wide binding profile of E2F4 using a newly developed peak calling program based on a kernel density estimation and identified approximately 16 thousands E2F4 binding sites at a 1% FDR threshold, which potentially modulate 7,346 downstream target genes. Gene Ontology (GO) functional analysis of E2F4 target genes revealed several novel functions of E2F4 including I-kappaB kinase/NF-kappaB cascade, protein transport and targeting, protein folding, and sterol biosynthetic process. In addition to mRNA target genes, E2F4 also binds and regulates some miRNA targets such as let-7a, mir-17 and mir-22. Interestingly, we found that about 20% of E2F4 sites are in intergenic regions, which suggests that E2F4 may function at enhancer sites. De novo motif discovery revealed 5 novel, significantly enriched motifs within E2F4 sites. Only 5% of binding sites contain a canonical motif, indicating that E2F4 can use diverse motifs to bind DNA and regulate transcription. Overexpression of E2F4 and its cofactors such as RBL2 and DP-1, followed by microarray analysis, revealed that E2F4 functions as an activator and a repressor. Taken together, our genome-wide E2F4 ChIP sequencing data provided evidences of versatile physiological roles of E2F4 and insights into its functions.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Identification of ploidy-regulated genes in budding yeast

first: Alex

last: Rolfe

address: 77 Massachusetts Ave, 32-G538

department: CSAIL

institute: Massachusetts Institute of Technology

summary: Using RNA-seq, we analyzed the transcriptomes of isogenic haploid (MATa) and tetraploid (MATaaaa) budding yeast strains in the Sigma 1278b background and identified genes whose regulation was altered by ploidy.

overall_design: Analysis of poly(A)+ RNA from 2 biological replicates of haploid (MATa) and tetraploid (MATaaaa) strains.

first: Chia-Yung

last: Wu

first: P

middle: K

last: Gifford

first: Gerald

last: Fink


title: E2F4 and its cofactor transfection vs empty vector transfection

summary: Transcriptional profiling of E2F4 target genes upon overexpression of E2F4 and it cofactors

overall_design: 4 conditions; E2F4 overexpression vs mock, E2F4 and DP-1 overexpression vs mock, E2F4 and RBL2 overexpression vs mock, E2F4, DP-1, and RBL2 overexpression vs mock. 2 or 4 replicates for each experimental conditions


title: A SNF2 protein targets variable copy number repeats and thereby influences allele-specific expression

city: Oxford

first: Richard

last: Gibbons

state: Oxon

address: John Radcliffe Hospital,

department: MRC Molecular Haematology Unit

institute: Weatherall Institute of Molecular Medicine

type: Genome binding/occupancy profiling by array

summary: ATRX is an X-linked gene of the SWI/SNF family whose role in vivo is currently unknown. Mutations in ATRX cause syndromal mental retardation. ATRX binds to tandem repeat (TR) sequences both in heterochromatin (e.g. telomeres) and euchromatin. Genes associated with these TRs can be dysregulated when ATRX is mutated and the degree to which their expression changes is determined by the size of the TR, producing skewed allelic expression. This explains the nature of the affected genes, the variable phenotypes seen with identical ATRX mutations and also illustrates a new mechanism underlying variable penetrance. Many of the TRs in ATRX targets are G-rich and predicted to form non-B DNA structures (including G quadruplex) in vivo. We have shown that ATRX binds G quadruplex structures in vitro suggesting a mechanism by which ATRX may play a role in various nuclear processes and how this is perturbed when ATRX is mutated.

overall_design:
4 Human Erythroblast, 1 HEP3B and 1 Fibroblast ChIP-ChIP Sample
For ChIP-Seq: one human erythroblasts, one mouse ES, one human erythroblast reference Sample, and one mouse ES input reference Sample.

first: Martin

last: Law

first: Karen

last: Lower

first: Hsiao

middle: P

last: Voon

last: Garrick

first: Vip

last: Viprakasit

first: Matthew

last: Mitson

first: Yongjun

last: Zhao

first: Jim

last: Hughes

first: Andrew

last: Morris

first: Aaron

last: Abbott

first: Steven

last: Wilder

first: Stephen

last: Taylor

first: Guilherme

last: Santos

first: Joe

last: Cross

first: Helena

last: Ayyub

last: Jones

first: Jiannis

last: Ragoussis

first: Daniela

last: Rhodes

first: Ian

last: Dunham

first: Douglas

last: Higgs


title: Histone H3K27ac separates active from poised enhancers and predicts developmental state

status: Public on Oct 31 2010

city: Rotterdam

first: Menno

last: Creyghton

address: Doctor Molewaterplein 40

country: Netherlands

institute: Erasmus MC

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


title: ChIP-Seq of chromatin marks at distal enhancers in Mouse Embryonic Stem Cells and adult tissues.

summary: Enhancers are enriched by histone H3 lysine 4 mono methylation (H3K4me1). To gain insight into the relation between enhancers and developmental state, chromatin immunoprecipitation coupled with massive parallel sequencing (ChIP-seq) was performed in several cell types to determine the genome-wide binding targets of H3K4me1 and several other possible enhancer associated modifications.

overall_design: DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing. A chromatin IP against histone H3 or whole cell extract was sequenced and used as the background to determine enrichment.  ChIP was performed mainly using antibodies against the chromatin marks H3K4me1 and H3K27ac.

first: Albert

middle: W

last: Cheng

first: Rudolf

last: Jaenisch


title: Double fragmentation ChIP-seq provides single nucleotide resolution Tcf4 binding characteristics

city: Utrecht

first: Michal

last: Mokry

address: Lundlaan 6

institute: Wilhelmina Children's Hospital, University Medical Center Utrecht

summary: ChIP-seq has become the method of choice for studying functional DNA-protein interactions on a genome wide scale. The method is based on co-immunoprecipitation of DNA binding proteins with formaldehyde cross-linked DNA, followed by deep sequencing of immunoprecipitated chromatin fragments, allowing for the identification of binding sites with high accuracy [1-5]. Traditionally, genome-wide tiling path microarrays were used for the detection of specifically immunoprecipitated DNA fragments, but current next-generation sequencers now generate sufficient data to assay multiple samples in a single sequencing run, making this method more time and cost effective compared to microarray-based approaches [2]. However, due to limitations in read length of next generation sequencing technologies (50-76bp), it is not possible to sequence the complete length of immunoprecipitated DNA fragments which can be up to 2kb long reflecting biology in case of big protein complexes. As a consequence only the ends of the immunoprecipitated DNA fragments are sequenced. Deconvolution of sequencing reads mapping to the positive and negative strand is required to identify the real DNA binding site [4-9]. This limitation is most obvious in case of large complex regions where multiple binding sites of various regulatory elements are clustered close to each other. Deconvolution of such regions and the exact identification of individual binding positions is very challenging [4]. Similar problems can occur when studying histone positioning in cases where the length of ChIP fragments is bigger than the average distance of 2 neighboring nucleosomes. In addition frequently only narrow size range of immunoprecipitated fragments is selected for sequencing and thus possible bias towards binding regions within the selected range can be expected by loosing larger fragments possible originated from protein complexes interacting with DNA. To circumvent these complications, we modified the procedure for the preparation of ChIP-seq samples by introducing an additional extensive fragmentation round after isolation of immunoprecipitated chromatin to generate 70-110 bp long DNA fragments. For testing, we choose Tcf4 protein which is a well-studied downstream element of the Wnt-pathway for which the genome wide binding site profile is known was already known from ChIP-on-CHIP experiments [10]. Using the modified approach, we were able to identify Tcf4 binding sites at near nucleotide resolution without computational deconvolution. Furthermore, high-resolution information on genome-wide binding site regions allowed for the identification of potential novel Tcf4 co-factors as well as target genes.

overall_design: 5 samples + 3 input samples


title: modENCODE_White Lab: genome-wide ChIP data of CG8478 from E16-24h on Illumina Genome Analyzer.

status: Public on Oct 30 2010

city: Chicago

first: Kevin

middle: P.

last: White

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

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 CG8478 from E16-24h 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

middle: A

last: Bild


title: Local DNA hypomethylation activates genes in rice endosperm

city: Berkeley

first: Toshiro

last: Nishimura

address: 211 Koshland Hall

department: Plant and Microbial Biology

institute: University of California at Berkeley

summary:
Cytosine methylation silences transposable elements in plants, vertebrates and fungi, but also regulates gene expression1. Plant methylation is catalyzed by three families of enzymes, each with a preferred sequence context: CG, CHG (H = A, C or T) and CHH, with CHH methylation targeted by the RNA interference (RNAi) pathway2. Arabidopsis thaliana endosperm, a placenta-like tissue that nourishes the embryo, is globally hypomethylated in the CG context while retaining high non-CG methylation3. Global methylation dynamics in seeds of cereal crops that provide the bulk of human nutrition remain unknown. Here we show that rice endosperm DNA is hypomethylated in all sequence contexts. Non-CG methylation is reduced evenly across the genome, while CG hypomethylation is localized. CHH methylation of small transposable elements is increased in embryos, suggesting that endosperm demethylation enhances transposon silencing. Genes preferentially expressed in endosperm, including those coding for major storage proteins and starch synthesizing enzymes, are frequently hypomethylated in endosperm, indicating that DNA methylation is a crucial regulator of rice endosperm biogenesis. Our data demonstrate that genome-wide reshaping of seed DNA methylation is conserved among angiosperms and has a profound effect on gene expression in cereal crops.

Keywords: Epigenetics

overall_design: Examination of DNA methylation in rice

first: Assaf

last: Zemach

first: M

middle: Y

last: Kim

first: Pedro

last: Silva

first: Jessica

last: Rodrigues

first: Bradley

last: Dotson

first: Matthew

middle: D

last: Brook

first: Daniel

last: Zilberman


title: A growth-essential Tetrahymena Piwi protein carries tRNA fragment cargo

status: Public on Oct 26 2010

city: Boston

first: Mary

middle: T

last: Couvillion

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

summary: Argonaute/Piwi proteins associate with small RNAs that typically provide sequence specificity for RNP function in gene and genome regulation. Here we show that Twi12, a Tetrahymena Piwi protein essential for growth, is loaded with mature tRNA fragments. The tightly bound ~18-22 nt tRNA 3’ fragments are biochemically distinct from the tRNA halves produced transiently in response to stress. Notably, the end positions of Twi12-bound tRNA 3' fragments precisely match RNAs detected in total small RNA of mouse embryonic stem cells and human cancer cells. Our studies demonstrate unanticipated evolutionary conservation of mature tRNA processing to tRNA-fragment small RNAs.

overall_design: Two libraries are analyzed here: sRNAs associated with slightly overexpressed ZZ-tagged Twi12 purified under native conditions (size range 15-34nt), and those associated after formaldehyde crosslinking (15-22nt).

first: Ravi

last: Sachidanandam

first: Kathleen

last: Collins


title: Differential genomic targeting of the transcription factor TAL1 in alternate hematopoietic lineages

first: Stephen

last: Tapscott

state: WASHINGTON

address: 1100 Fairview N. Ave

department: Human Biology

institute: Fred Hutch Cancer Research Center

summary: TAL1/SCL is a master regulator of hematopoiesis whose expression promotes opposite outcomes depending on the cell type - differentiation in the erythroid lineage or oncogenesis in the T-cell lineage. Here we used a combination of ChIP-sequencing and gene expression profiling to compare the function of TAL1 in normal erythroid and leukemic T-cells. Analysis of the genome-wide binding properties of TAL1 in these two hematopoietic lineages revealed new insight into the mechanism by which transcription factors select their binding sites in alternate lineages. Our study shows limited overlap in the TAL1 binding profile between the two cell types with an unexpected preference for ETS and RUNX motifs adjacent to E-boxes in the T-cell lineage. Furthermore we show that TAL1 interacts with RUNX1 and ETS1, and that these transcription factors are critically required to target TAL1 to genes that modulate T-cell differentiation. Thus, our findings highlight a critical role of the cellular environment in modulating transcription factor binding, and provide insight into the mechanism by which TAL1 inhibits differentiation leading to oncogenesis in the T-cell lineage.

overall_design: Examine TAL1/SCL binding sites in two different cell lineages (i.e. primary human pro-erythroblasts and the Jurkat T-ALL cell line). These records represent the ChIP-seq part of the study. The gene expresssion part is available at GSE20546.

first: Marjorie

last: Brand

first: Zizhen

last: Yao


title: Transcription profile of the Plasmodium falciparum intraerythrocytic cycle

status: Public on Oct 28 2010

city: Nijmegen

last: Stunnenberg

address: Geert Grooteplein 28

department: Department of Molecular Biology (274)

institute: Radboud University

summary: This experiment characterizes the transcriptome of the human malaria parasite, P. falciparum at 8 different stages of the intraerythrocytic cycle

overall_design: Examination of polyA selected RNA in Plasmodium falciparum 3D7 strain at 8 different stages using RNA-seq

first: Richard

last: Bartfai

first: Wieteke

last: Hoeijmakers

first: Adriana

last: Salcedo-Amaya

first: Arne

middle: H

last: Smits

first: Eva

last: Janssen-Megens

first: Anita

last: Kaan

first: Moritz

last: Treeck

first: Tim-Wolf

last: Gilberger

first: Kees-Jan

last: Françoijs

first: Hendrik


title: Representative Illumina sequencing libraries upon T7-polymerase based amplification

summary: This experiment highlights the extreme sequence bias generated by standard PCR amplication of sequencing libraries and decribes an adapted T7-polymerase based amplification method, which results in non-baised, representative libraries for Illumina sequencing

overall_design: Adaptation of standard Illumina sequencing protocol to obtain representative sequencing libraries after sample amplification. Comparing different amplification methods with amplification free sequencing.


title: Developmental gene regulation by an ancient intercellular communication system in social amoebae

status: Public on Oct 29 2010

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

country: Germany

institute: Leibniz Institute on Aging - FLI

summary:
In the social amoebae (Dictyostelia) quorum sensing system mediates aggregation of single cells into multicellular aggregates by chemotactic movement towards gradients of diffusible molecules known as acrasins. The acrasin of P. violaceum is the unusual dipeptide N-propionyl-gamma-L-glutamyl-L-ornithine-delta-lactam-ethylester, known as glorin. Phylogenetic analysis has indicated that P. violaceum is more related to the most derived group 4 dictyostelids than to the ancient group 2 polysphondylids such as P. pallidum. Nevertheless it has been reported that P. pallidum cells respond to glorin in chemotaxis assays. This has led to the assumption that glorin-based communication may be the most ancient form of intercellular communication that Dictyostelia invented to organize early steps of multicellular development. In this study we show that glorin mediates rapid changes in gene expression at the transition from vegetative growth to aggregation, apparently without pronounced cross-talk with the cyclic AMP-based communication system that coordinates post-aggregation events in this species.

We describe glorin-mediated changes in gene expression in the social amoeba Polysphondylium pallidum at the transition from unicellular growth to multicellular development.

overall_design: Comparison of gene expression in growing cells versus cells starving for 2 or 3 hours in the presence or absence of glorin.

first: Thomas

last: Winckler


title: Deep sequencing of the innate immune transcriptomic response of zebrafish embryos to Salmonella infection

city: Amsterdam

first: Oliver

last: Stockhammer

state: NH

address: Meibergdreef 15

department: Medical Microbiology

institute: AMC

summary: Salmonella enterica serovar Typhimurium (S. typhimurium) bacteria cause an inflammatory and lethal infection in zebrafish embryos. To characterize the embryonic innate host response at the transcriptome level, we have extended and validated previous microarray data by Illumina next-generation sequencing analysis. Comparison of tag-based sequencing (DGE or Tag-Seq) with full transcript sequencing (RNA-Seq) showed a strong correlation of sequence read counts per transcript and an overlap of 241 transcripts differentially expressed in response to infection. A slightly lower overlap of 165 transcripts was observed with previous microarray data. Based on the combined sequencing-based and microarray-based transcriptome data we compiled an annotated reference set of infection-responsive genes in zebrafish embryos, encoding transcription factors, signal transduction proteins, cytokines and chemokines, complement factors, proteins involved in apoptosis and proteolysis, proteins with anti-microbial activities, as well as many known or novel proteins not previously linked to the immune response. Furthermore, by comparison of the deep sequencing data of S. typhimurium infection in zebrafish embryos with previous deep sequencing data of Mycobacterium marinum infection in adult zebrafish we derived a common set of innate host defense genes that are expressed both in the absence and presence of a fully developed adaptive immune system and that provide a valuable reference for future studies of host-pathogen interactions using zebrafish infection models.

overall_design: Zebrafish embryos were infected with Salmonella typhimurium (strain SL1027) by microinjection of DsRED-labeled bacteria into the caudal vein close to the urogenital opening after the onset of blood circulation (27 hpf). An equal volume of PBS was injected in the control group. RNA samples were collected at 8 hours post infection (hpi) and samples from triplicate infection experiments were pooled. DGE libraries from the RNA pools (1 μg) of Salmonella-infected and control embryos were prepared using the DGE:Tag Profiling for NlaIII Sample Prep kit from Illumina as previously described (Hegedus et al., 2009). The libraries were sequenced in duplicate using 2 (Control 1; Salmonella infected 1) and 3 pmol (Control 2; Salmonella infected 2) of cDNA. Sequencing was performed using the Illumina Genome Analyzer II System (BaseClear B.V., Leiden, The Netherlands) according to the manufacturer’s protocols. Image analysis, base calling, extraction of 17 bp tags and tag counting were performed using the Illumina pipeline. Tag counts from duplicate libraries were merged in silico.

last: Ordas

first: Zoltán

last: Hegedűs

first: Christian

middle: V

last: Henkel

first: Derek

last: Butler

first: Hans

last: Jansen

first: Peter

middle: I

last: Racz

first: Matyas

last: Mink

first: Herman

last: Spaink

first: Annemarie

last: Meijer


title: Probing the initiation and effector phases of the somatic piRNA pathway in Drosophila

status: Public on Oct 25 2010

city: Cold Spring Harbor

first: Astrid

last: Haase

address: One Bungtown Road

institute: Cold Spring Harbor Laboratory

summary: Combining RNAi in cultured cells and analysis of mutant animals, we probed roles of known piRNA pathway components in the initiation and effector phases of transposon silencing.

overall_design: total RNA and RNA associated with Piwi was isolated and size-fractionated by PAGE into 19-29nt. These were processed and sequenced on Illumina Genome Analyzer II.

first: Silvia

last: Fenoglio

first: Felix

last: Muerdter

first: Paloma

last: Guzzardo

first: Benjamin

last: Czech

first: Darryl

last: Pappin

first: Caifu

last: Chen

first: Assaf

last: Gordon

first: Gregory

last: Hannon


title: Deep-transcriptome and ribonome sequencing redefines the molecular networks of pluripotency and the extracellular space in human Embryonic Stem cells

status: Public on Oct 20 2010

city: St Lucia

first: Sean

last: Grimmond

state: Q

address: Services Rd

department: Institute for Molecular Bioscience

country: Australia

institute: University of Queensland

summary: Cytoplasmic polyadenylated RNA from human embryonic stem cells (HES2) was separated on a 1.2% agarose and gel slices were excised corresponding to the following sizes: 0 to 0.5 kb; 0.5-2 kb; 2-3.5 kb; 3.5-6.5 kb and 6.5-20+ kb. Slices were dissolved and extracted RNA (1% of each fraction) was run on the Agilent Bioanalyser (Agilent) to confirm the correct size distribution and yield. Library molecules were clonally amplified onto one micron magnetic beads according to the SOLiD Template Bead Preparation protocol and sequenced using a SOLiD Analyzer according to manufacturer's instructions.

overall_design: Human ES cells size fractionated mRNA

first: Gabriel

last: Kolle


title: Genome-wide mapping of PRDM14 binding sites in human embryonic stem cells

city: Singapore

first: Yuriy

last: Orlov

address: 60 Biopolis Street

department: Computational Systems Biology

country: Singapore

institute: Genome Institute of Singapore

summary: PRDM14 belongs to the PR (PRDI-BF1 and RIZ) domain proteins (PRDM) family which is a subclass of the SET domain proteins, a common domain found in histone modifying enzymes. PRDM14 has been previously implicated to regulate self-renewal of hESCs as knock-down of PRDM14 induced expression of differentiation marker genes and altered the cellular morphology. We showed that PRDM14 directly regulates the expression of key pluripotency gene POU5F1. Genome-wide location profiling experiments revealed that PRDM14 co-localized extensively with other key transcription factors such as OCT4, NANOG and SOX2. More importantly, in a gain-of-function assay, we showed that PRDM14 is able to enhance the efficiency of reprogramming of human fibroblasts in conjunction with OCT4, SOX2 and KLF4. Hence, PRDM14 exemplifies a key transcription factor that is required for the maintenance of human ESC identity and the reacquisition of pluripotency in human somatic cells.

overall_design: ChIP-seq of PRDM14 in human ESCs

first: Huck-Hui

last: Ng

first: Yuin-Shen

last: Chan

first: Na-Yu

last: Chia