title: Arabidopsis lyrata small RNAs

city: University Park

first: Michael

last: Axtell

state: PA

address: 280 Mueller Lab

institute: Pennsylvania State University

summary: Small RNA sequences from Arabidopsis lyrata leaves, as isolated from a single sample of rosette leaf tissue.  These data were analyzed to 1) examine microRNA processing accuracy in A. lyrata and 2) to examine patterns of 24nt siRNA accumulation in A. lyrata.

overall_design: A single small RNA library from rosette leaf tissue was analyzed using an Illumina Genome Analyzer.

first: Zhaorong

last: Ma

first: Ceyda

last: Coruh


title: Phenotypic plasticity in the pea aphid Acyrthosiphon pisum

status: Public on Mar 01 2010

city: Rennes

first: Stephanie

last: Jaubert

address: domaine de la Motte

country: France

institute: INRA

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: MicroRNAome of porcine prenatal and postnatal development.

status: Public on Feb 27 2010

city: Ya'an

first: Mingzhou

last: Li

state: Sichuan

address: No.46  Xinkang Road

department: College of Animal Science and Technology

country: China

institute: Sichuan Agricultural University

summary: Sus scrofa (pig, or swine) is one of the most important economic animals and a close biological model for complex human diseases such as obesity and diabetes. It is therefore utterly important to decode the porcine microRNAome (miRNAome) as in the literature only a small portion of it is known. In this work, a comprehensive search for porcine microRNAs (miRNAs) by Illumina sequencing was performed in ten small RNA libraries prepared from mixtures of assorted tissues, which included those collected from fetuses to adult pigs. The millions of the sequencing reads were analyzed with reference to 77 known porcine miRNA precursors (pre-miRNAs) and 3,443 distinct pre-miRNAs of other mammals listed in miRBase 13.0, and the most updated porcine genome (Sscrofa9, April 2009) and available EST sequences. Additionally, miRNA candidates specific to pig are predicated by genome & EST match and hairpin folding. Our search found 72 out of 78 (~92%) known porcine miRNAs and miRNA*s, and 36 previously unannotated miRNA*s are also indentified. Furthermore, we discovered 397 novel miRNAs by mapping to the sequencing transcripts to other mammalian pre-miRNAs and 493 candidate miRNAs which do not map to other mammalian miRNAomes and could be pig-specific. We constructed sequence- and genome-position clusters for the total of 998 miRNA candidates originating from 862 pre-miRNAs, which represent 777 unique miRNA sequences. Together with the six known porcine miRNAs that not been observed in our study, we report herein the sequence families of 783 unique miRNAs and genomic distribution patterns of 622 pre-miRNAs. We preformed q-PCR experiments for selected 30 miRNAs in 47 tissue-specific samples and found agreement between the sequencing data and the q-PCR data. We envision that our report will serve as a valuable resource for future studies aimed at understanding miRNAome of pig

overall_design: Ten small RNA libraries from samples of porcine fetuses (30 days after insemination) to mixed tissues (180 days after birth) at ten developmental stages were sequenced.

first: Youlin

last: Xia

first: Yiren

last: Gu

first: Kai

last: Zhang

first: Xiaolian

last: Gao

first: Xuewei


title: rice whole transcriptome surveyed by RNA-Seq and Paired-end technology

city: Shenzhen

first: Guangwu

last: Guo

state: Guangdong Province

address: Main Building,Beishan Industrial Zone, Yantian District

department: Bioinformatics center

institute: Beijing Genomics Institute at Shenzhen

summary:
Transcriptome analysis is an important approach to associate genotype with phenotype. The content and dynamics of eukaryotic transcriptome are far more complex than previously anticipated. Here we integrated high-throughput RNA-seq and paired-end method to conduct an unprecedentedly deep survey of transcription profile for cultivated rice, one of the oldest domesticated crops species and has since spread worldwide to become one of the major staple foods. Analysis of reads mapping revealed 4,244 previously uncharacterized transcripts, including a mass of protein-coding genes and putative functional non-coding RNA genes. Alignment of junction reads indicated over 42% of rice multiple-exon genes produce two or more distinct splicing isoforms. It’s intriguing that we identified 1,356 putative gene fusion events, indicating the 234 fusion gene produced by trans-splicing vastly increases the complexity of rice transcriptome, together with the pervasive alternative splicing events. Digital gene expression profiling revealed most rice duplicate genes were maintained by the selection constraint on gene dosages, which would increase the genetic robustness of rice to counteract deleterious mutations

Keywords: Expression profiling by high throughput sequencing

overall_design: mRNA expression of 8 independent rice tissues was determined by method of RNA-Seq using short reads from high throughput sequencing technology. Meanwhile small RNA populations from mixture solution pooled from total RNA of each 8 tissues were also sequenced.

first: Guojie

first: Xueda

last: Hu

first: Qiye

first: Ruhong

last: Zhuang

first: Wei

last: Tian

first: Quanfei

last: Huang

first: Zengquan

last: He

first: Yong

last: Tao


title: Identification and analysis of miRNA target genes in a cell system

status: Public on Mar 17 2010

city: New York

first: Thomas

last: Templin

state: NY

address: 630 West 168th Street

country: USA

institute: Columbia University Medical Center

summary: MicroRNAs are instructions used by the genetic programs of a cell to fine-regulate protein expression levels. In order to gain insight into the full spectrum of miRNA regulation in a particular cellular context, we have exploited the idea that doubling the quantity of the endogenous miRNAs by transfection would enhance downregulation of the normally targeted transcripts. To this end, we isolated the small RNA fraction from cells in culture and transfected it into an identical culture in an amount corresponding to that of the endogenous miRNAs. A comparative gene expression analysis between transfected and mock-transfected cells revealed a large number of modestly downregulated genes. In silico analysis using TargetScan 5 revealed that a very high number of the expressed genes are predicted targets of the endogenous miRNAs, which we identified by deep-sequencing the small RNA fraction. Network analysis of the downregulated genes showed that miRNAs are involved in the simultaneous regulation of many pathways by targeting key molecules that interact with multiple pathways, suggesting a role of miRNAs in the synchronization of the activities of different pathways. Interestingly, we found a very high percentage of the genes regulated by miRNAs to be related to genetic disorders. This suggests that miRNAs might play a key role in maintaining homeostasis in processes that result in disease states when disregulated. Such a crucial role for miRNA regulation further underlines its importance for cell and organism survival. These results also confirm the important experimental value of our methodology as a high throughput tool for the identification of genes endogenously regulated by miRNAs.

overall_design: We isolated the small RNA fraction (20-200 bp) from one culture of normal human fibroblasts and performed quantitative deep sequencing on the Illumina/Solexa platform. We obtained a total of 19E06 sequences, which were blasted against mRNA, RFAM and repbase. The result revealed that the content of this fraction was shared (in % copy numbers) by rRNA: 1.03%, tRNA: 2.3649%, snRNA: 0.0611%, snoRNA: 1.3803%, mRNA: 1.8183%, ncRNA mapped to Rfam: 6.0411%, sequences mapped to repbase: 3.4146%, and the remaining 83% were pre-miRNA and miRNA.  A total of 702 human miRNAs were detected. This number was reduced to 324 after filtering out all miRNAs with a copy number of less than 3.

first: Sally

middle: A

last: Amundson

first: Shanaz

last: Ghandhi

first: Guangming

last: Zhou

first: Lubomir

middle: B

last: Smilenov


title: Biochemical Identification of Targets of Individual MicroRNAs in Mouse Embryonic Stem Cells

city: Cambridge

first: Sophie

middle: Alexandra

last: Hanina

state: Cambridgeshire

address: Tennis Court Road

department: Gurdon Institute

country: United Kingdom

institute: University of Cambridge

summary: Mouse Embryonic Stem (ES) cells express a unique set of microRNAs (miRNAs), the miR-290-295 cluster. To elucidate the role of these miRNAs and how they integrate into the ES cell regulatory network requires identification of their direct regulatory targets. The difficulty, however, arises from the limited complementarity of metazoan miRNAs to their targets, with the interaction requiring as few as six nucleotides of the miRNA seed sequence. To identify miR-294 targets, we used Dicer1-null ES cells, which lack all endogenous mature miRNAs, and introduced just miR-294 into these ES cells. We then employed two approaches to discover miR-294 targets in mouse ES cells: transcriptome profiling using microarrays, and a biochemical approach to isolate mRNA targets associated with the Argonaute2 (Ago2) protein of the RISC (RNA Induced Silencing Complex) effector, followed by RNA-Sequencing. In the absence of Dicer1, the RISC complexes are largely devoid of mature miRNAs, and should therefore contain only transfected miR-294 and its base-paired targets. Our data suggest that miR-294 may promote pluripotency by regulating a subset of c-Myc target genes, and upregulating pluripotency-associated genes such as Lin28.

overall_design: For RNA-IP experiments, cells were transfected with 300 pmol of miR-294 or cel-239b control miRNA (Dharmacon) and harvested 12-16 hr after transfection for immunoprecipitation. Following RNA-immunoprecipitation of Ago2-myc, RNA from the INPUT (total RNA) and IP were subjected to library preparation and sequenced by SOLiD. There are 10 samples from Dicer1-null mouse ES cells, which are essentially 5  sample pairs of INPUT (A) and its corresponding RNA-IP (B): Ago2-myc transfected with miR-294 (sampe 1), 2 replicates of Ago2-myc-MUT (catalytically inactive) transfected with miR-294 (sample 2 & 5), 2 replicates of Ago2-myc transfected with cel-239b (sample 3 & 4).

first: William

last: Mifsud

last: Down

first: Kaiqin

last: Lao

first: M

last: Surani


title: Genome-wide analysis of alternative splicing evolution among Mus subspecies

status: Public on Feb 28 2010

city: Ploen

first: Bettina

last: Harr

address: August-Thienemannstrasse 2

country: Germany

institute: Max-Planck-Institute for Evolutionary Biology

type: Expression profiling by high throughput sequencing

summary: We studied the evolution of alternative splicing in the early stages of species divergence in the house mouse.

sample_organism:
Mus musculus castaneus
Mus musculus domesticus
Mus spretus
Mus musculus musculus

overall_design: We sequenced the testis transcriptomes of three Mus musculus subspecies and Mus spretus using Illumina technology. On the basis of a genome-wide analysis of read coverage differences among subspecies, we identified several hundred candidate alternatively spliced regions.

first: Leslie

middle: M

last: Turner


title: Sequential rounds of RNA-dependent RNA transcription drive endogenous small-RNA biogenesis in ERGO-1/Argonaute pathway

status: Public on Feb 25 2010

city: Worcester

first: Craig

last: Mello

state: MA

address: 368 Plantatoin Street, Suite AS5-2047

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

summary: Argonaute (AGO) proteins interact with distinct classes of small RNAs to direct multiple regulatory outcomes. In many organisms, including plants, fungi and nematodes, cellular RNAdependent RNA polymerases (RdRPs) utilize AGO targets as templates for amplification of silencing signals. Here, we show that distinct RdRPs function sequentially to produce small RNAs that target endogenous loci in C. elegans. We show that DCR-1, the RdRP RRF-3, and the dsRNA-binding protein RDE-4, are required for the biogenesis of 26nt RNAs, termed 26GRNAs, and that 26G-RNAs engage the Piwi-clade AGO, ERGO-1. Our findings support a model in which targeting by ERGO-1 recruits a second RdRP (RRF-1 or EGO-1), which in turn transcribes 22G-RNAs that interact with worm-specific AGOs (WAGOs) to direct gene silencing. ERGO-1 targets exhibit a non-random distribution in the genome and appear to include many gene duplications, suggesting that this pathway may control over-expression resulting from gene expansion.

overall_design: 8 samples examined. Small RNA libraries generated from: C. elegans animals.

first: Jessica

last: Vasale

first: Weifeng

last: Gu

first: Darryl

last: Conte

middle: C


title: AGO pathway

status: Public on Feb 24 2010

type: Expression profiling by genome tiling array


title: Genome-wide maps of AGO1-bound small RNA in Arabidopsis leaves

city: Beijing

first: Jianmin

address: # Science Park road,Zhongguancun Life Science Park,Beijing

institute: National Institute of Biological Sciences, Beijing

summary: We report flg22 regulate the accumulation of AGO1-bound small RNA in arabidopsis. We find that a number of miRNAs are up- or down-regulated by flg22, a well-studied PAMP.

overall_design: Examination of AGO1-bound small RNAs with or without flg22 treatment.

first: Yan

last: Li

first: Qingqing

last: Zhang

first: Jianguang

first: Liang

last: Wu

first: Yijun

last: Qi


title: Understaning mechanisms underlying human gene expression variation with RNA sequencing

city: Chicago

first: Joseph

last: Pickrell

state: IL

institute: University of Chicago

summary: Understanding the genetic mechanisms underlying natural variation in gene expression is a central goal of both medical and evolutionary genetics, and studies of expression quantitative trait loci (eQTLs) have become an important tool for achieving this goal. While all eQTL studies to date have assayed mRNA levels using expression microarrays, recent advances in RNA sequencing enable the analysis of transcript variation at unprecedented resolution. We sequenced RNA from 69 lymphoblastoid cell lines (LCLs) derived from unrelated Nigerian individuals that have been extensively genotyped by the International HapMap Project. Pooling data from all individuals, we generated a map of the transcriptional landscape of these cells, identifying extensive use of unannotated polyadenylation sites and over 100 novel putative protein-coding exons.  Using the genotypes from the HapMap project, we identified over a thousand genes at which genetic variation influences overall expression levels or splicing. We demonstrate that eQTLs near genes generally act via a mechanism involving allele-specific expression, and that variation that influences the inclusion of an exon is enriched within or near the consensus splice sites. Our results illustrate the power of high-throughput sequencing for the joint analysis of variation in transcription, splicing, and allele-specific expression across individuals.

overall_design: RNA-Seq in 69 lymphoblastoid cell lines from multiple Yoruban HapMap individuals in at least two replicate lanes per individual

first: Jonathan

last: Pritchard

first: Yoav

last: Gilad


title: Argonaute Surveillance and Dicer-Independent priRNAs TriggerRNAi and Heterochromatin Formation

status: Public on Feb 23 2010

city: Munich

first: Mario

last: Halic

address: Feodor-Lynenstr. 25

department: Department of Biochemistry

institute: Gene Center, University of Munich

summary: The assembly of fission yeast pericentromeric heterochromatin and generation of small interfering RNAs (siRNAs) from noncoding centromeric transcripts are mutually dependent processes. How this interdependent positive feedback loop is first triggered is a fundamental unanswered question. Here we show that two distinct Argonaute (Ago1)-dependent pathways mediate small RNA generation. RNA-dependent RNA polymerase complex (RDRC) and Dicer act on specific noncoding RNAs to generate siRNAs by a mechanism that requires the slicer activity of Ago1 but is independent of pre-existing heterochromatin. In the absence of RDRC or Dicer, a distinct class of small RNAs, called primal small RNAs (priRNAs), associate with Ago1. priRNAs are degradation products of abundant transcripts, which bind to Ago1 and target antisense transcripts that result from bidirectional transcription of DNA repeats. Our results suggest that a transcriptome surveillance mechanism based on the random association of RNA degradation products with Argonaute triggers siRNA amplification and heterochromatin assembly within DNA repeats.

overall_design: small RNA profiling in wild type S. pombe cells and in 12 mutant cells

first: Danesh

last: Moazed


title: Regulatory Divergence in Drosophila revealed by mRNA-seq

status: Public on Feb 20 2010

city: Farmington

first: Brenton

middle: R

last: Graveley

state: CT

address: 400 Farmington Avenue

department: Genetics and Genome Sciences

institute: University of Connecticut Health Center

summary:
These data were generated in a study to analyze the genetic causes of gene regulatory divergence.  mRNA-seq libraies were prepared from poly(A)+ RNA prepared from whole F1 hybrids of D. melanogaster and D.   sechellia (female 0-3d post eclosion, "D_mel_x_D_sec").  A mixed mRNA- seq library was prepared  from D. melanogaster and D. sechellia poly(A) + RNA (mixed before library preparation, "D_mel_+_D_sec). Finally, separate mRNA-seq libraries were prepared from poly(A)+ RNA from each species ("D_mel" and "D_sec").  The results of this study showed that 78% of genes expressed in the two species are differentially expressed, and that cis- and trans-regulatory divergence affect 51% and 66% of expressed genes, respectively.

Keywords: RNA-Seq

sample_organism: Drosophila melanogaster x Drosophila sechellia

overall_design: There were 4 total samples in this study.  mRNA-seq was used to measure allele-specific gene expression levels from 9966 genes in the F1 hybrid, and mixed samples.  Comparisons of relative gene expression levels between species and allele-specific expression levels within the F1 hybrid were used to assay the contributions of cis- and trans-regulatory divergence between the species.

first: C

middle: J

last: McManus

middle: D

last: Coolon

first: Jodi

last: Eipper-Mains

first: Michael

middle: O

last: Duff

first: Patricia

last: Wittkopp


title: Nuclear retention of fission yeast dicer is a prerequisite for RNAi-mediated heterochromatin assembly

status: Public on Feb 16 2010

city: Basel

first: Dimos

last: Gaidatzis

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

summary: RNAseIII ribonucleases act at the heart of RNA silencing pathways by processing precursor RNAs into mature microRNAs and siRNAs. In the fission yeast Schizosaccharomyces pombe, siRNAs are generated by the RNAseIII enzyme Dcr1 and are required for heterochromatin formation. In this study, we have analyzed the subcellular localization of Dcr1 and found that it accumulates in the nucleus and is enriched at the nuclear periphery. Nuclear accumulation of Dcr1 depends on a short motif which constrains nuclear export promoted by the double-stranded RNA binding domain of Dcr1. Absence of this motif renders Dcr1 mainly cytoplasmic and is accompanied by remarkable changes in gene expression and failure to assemble heterochromatin. Our findings suggest that dicer proteins are shuttling proteins and that the steady-state subcellular levels can be shifted towards either compartment. This has implications for the mechanism of RNAi-mediated heterochromatin assembly and the spatial organization of RNA silencing pathways in general.

overall_design: Small RNA libraries from total RNA isolations of wild-type, dcr1Delta and dcr1DeltaC33 cells and subjected to high-throughput sequencing.

first: Stephan

last: Emmerth

first: Heiko

last: Schober

first: Kirsten

last: Jacobeit

first: Marc

last: Bühler


title: Small RNA of the model grass Brachypodium distachyon

status: Public on Feb 15 2010

city: Saint Louis

first: James

last: Carrington

state: MO

address: 975 North Warson Road

institute: Donald Danforth Plant Science Center

summary: Deep sequencing of Brachypodium distachyon small RNA from panicles (flowers) was done to analyze the genome-wide distribution patterns of 1) total small RNA reads and loci, 2) 21 and 24 nucleotide repeat-normalized reads and 3) 21 and 24 nucleotide phased siRNA clusters relative to gene and transposable element density.

overall_design:
Small RNA were extracted from total RNA by size fractionation and converted to DNA amplicons by serial adaptor ligation to both ends followed by RT-PCR.  DNA amplicons were sequenced using an Ilumina Genome Analyzer.  Resulting sequences were computationally trimmed to remove 3' adaptor sequences.

Raw data for GSM506621 was not provided.

first: Noah

last: Fahlgren

first: Samuel

middle: E

last: Fox

first: Christopher

last: Sullivan

first: Todd

last: Mockler

first: Elisabeth

last: Chapman

first: Greg

last: May

first: Jixian

last: Zhai

first: Matthias

last: Ganssmann

first: Sai

middle: G

last: Gurazada

first: Marcelo

last: German

first: Blake

last: Meyers

first: Pamela

last: Green


title: Small RNA expression and strain specificity in the rat

status: Public on Feb 17 2010

city: Utrecht

first: Sam

last: Linsen

address: Uppsalalaan 8

department: Genome Biology

country: Netherlands

institute: Hubrecht Institute

summary: Background  Digital gene expression (DGE) profiling has become an established tool to study RNA expression. Here, we provide an in-depth analysis of small RNA DGE profiles from two different rat strains (BN-Lx and SHR) from six different rat tissues (spleen, liver, brain, testis, heart, kidney). We describe the expression patterns of known and novel micro (mi)RNAs and piwi-interacting (pi)RNAs. We confirmed the expression of 589 known miRNAs and identified 56 miRNAs homologous to known human or mouse miRNAs, as well as 45 new rat miRNAs. Furthermore, we confirmed specific A to I editing in brain for mir-376a/b/c and identified mir-377 as a novel editing target. In accordance with earlier findings, we observed a highly tissue-specific expression pattern for all tissues analyzed. The brain was found to express the highest number of tissue-specific miRNAs, followed by testis. Notably, our experiments also revealed robust strain-specific differential miRNA expression in the liver that is caused by genetic variation between the strains. Finally, we identified two types of germline-specific piRNAs in testis, mapping either to transposons or in strand-specific clusters. Taken together, the small RNA compendium described here advances the annotation of small RNAs in the rat genome. Strain and tissue-specific expression patterns furthermore provide a strong basis for studying the role of small RNAs in regulatory networks as well as biological process like physiology and neurobiology that are extensively studied in this model system.

overall_design: Small RNAs from 6 tissues were cloned and sequenced. Tissues included whole brain, liver, spleen, heart, testis, kidney. Tissues were sequenced from 2 rats: one BN-Lx rat and one SHR rat. For strain-specific miRNA expression we included 4 replicate whole livers, i.e. from 2 BN-Lx rats and 2 SHR rats.

first: Elzo

last: de Wit

first: Ewart

last: de Bruijn

first: Edwin

last: Cuppen


title: Genome-wide map of PCL2 (Polycomb-like 2) enrichment in undifferentiated mouse embryonic stem cells (ESCs)

status: Public on Feb 05 2010

city: Toronto

first: William

middle: L

last: Stanford

state: Ontario

address: 164 College St

department: IBBME

country: Canada

institute: University of Toronto

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
In total 8,736,191 reads from IP fraction and 9,958,984 reads from Wash fraction uniquely mapped to the mouse genome (mm9). Settings for enrichment analysis: maxSpacing=500; minHits=20; minPeakHits=6; minRatio=3. 4,701 regions have been identified as enriched in the IP fraction. In order to get a rough idea of false discovery rate (FDR), enrichment analysis using Wash fraction as test and IP fraction as control was performed, 15 regions was found. This suggests that the FDR likely is around 0.3%.

Keywords: Epigenetics

overall_design: Examination of PCL2 enrichment in mouse ESCs.

first: Emily

last: Walker

first: Wing

middle: Y

last: Chang


title: In depth sequencing of the siRNAs associated with peach latent mosaic viroid infection

city: Sherbrooke

first: Jean-Pierre

last: Perreault

state: Québec

address: 3001, 12ième avenue Nord

department: Biochimie

institute: Université de Sherbrooke

summary: Using a high-throughput sequencing approach we quantitatively analyzed the content of viroid-derived siRNAs of an infected tree. Our results show that the entire PLMVd genome is found in the siRNA population. Also both polarities are susceptible to be targeted by the RNAi machinery but specific regions for each polarity are over represented. Those regions, that are not the same for each polarity, do not necessarily correlate with double stranded regions that could be substrate for Dicer-like enzymes. Finally the analysis of the first 5’ nucleotide revealed a bias toward a C or a U in viroid-derived siRNAs, indicating that at least AGO5 and AGO1 can recruit these small RNAs.

sample_organism:
Prunus persica
Prunus persica var. nucipersica

overall_design: Analysis of siRNAs population from RNA sample isolated from a viroid-infected tree

first: François

last: Bolduc

first: Christopher

last: Hoareau

first: Patrick

last: St-Pierre


title: RNA-Seq of melanoma short-term cultures and cell lines

status: Public on Feb 04 2010

first: Michael

last: Berger

address: 7 Cambridge Center

department: Cancer Program

institute: The Broad Instititute

summary: Identification of RNA-based alterations in melanoma by RNA-Seq, including gene fusions, sequence mutations, and aberrant gene expression levels (to compare to expression level estimates obtained by microarray).

overall_design: melanoma short-term cultures and cell lines were propagated in vitro, and total RNA was extracted for sequencing

first: M

middle: F

first: Levi

last: Garraway


title: Regulation of alternative splicing by histone modifications

status: Public on Feb 10 2010

first: Qun

last: Pan

address: 160 College St.

summary: Alternative splicing of pre-mRNA is a prominent mechanism to generate protein diversity, yet its regulation is poorly understood. Here, we demonstrate a direct role for histone modifications in alternative splicing. We find distinctive histone modification signatures which correlate with splicing outcome in a set of human genes. Modulation of histone modifications causes splice site switching. The mechanism for histone-mediated splice site selection involves a histone mark which is read by a chromatin protein, which in turn recruits a splicing regulator. These results outline an adaptor system for reading of histone marks by the pre-mRNA splicing machinery.

overall_design: To obtain an estimate of how many PTB-dependent alternative splicing events are regulated by SET2/MRG15-mediated recruitment of PTB, we carried out a genomewide comparative analysis of alternative splicing in hMSC cells depleted of either SETD2, MRG15 or PTB using specific siRNAs, or mock-depleted using a control siRNA.

first: Reini

last: Luco

first: Kaoru

last: Tominaga

first: Benjamin

last: Blencowe

first: Olivia

last: Pereira-Smith

first: Tom

last: Misteli


title: Highly efficient genomic enrichment of human exonic sequences through short-fragment libraries

status: Public on Feb 01 2010

first: Michal

last: Mokry

address: Lundlaan 6

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

summary: Microarray-based enrichment of selected genomic loci is a powerful method for genome complexity reduction. Since the vast majority of exons in vertebrate genomes are smaller than 150 nt, we have explored the use of short fragment libraries (85-110bp) to achieve higher enrichment specificity by reducing carryover and adverse effects of flanking intronic sequences. These short fragment libraries were enriched for 1.69 Mb of exonic sequences, using custom 244K microarrays, and sequenced using AB/SOLiD. High enrichment specificity (60 – 75%) was obtained at 67-213x average coverage, with 77-92% and 90-98% of targeted regions covered with more than 25% and 10% of the average coverage, respectively. As a more appropriate measure of the evenness of coverage, which is relatively independent of sequencing depth, we introduce the evenness of coverage parameter E. E values up to 75% were achieved. To verify the accuracy of SNP/mutation detection we evaluated 384 known non-reference SNPs in the targeted regions. At ~ 200x average sequence coverage, we were able to survey 96.4% of 1.69 Mb of genomic sequence with only 4.2% false negative calls while 3.6% of targeted regions were marked as unsurveyed. A total of 1197 new variants were detected. Verification revealed only 8 false positive calls, resulting in an overall false positive rate of less than 1 per ~200,000 bp (0.0005%, equivalent to an overall phred score of 55).

overall_design: 4 samples + capture design file


title: Transcriptome of Aspergillus oryzae following ER stress

status: Public on Feb 02 2010

first: Guangwu

last: Guo

summary: The Aspergillus oryzae, an important filamentous fungus used in food fermentation and enzyme industry, has been revealed to own prominent features in its genomic compositions by genome sequencing and various other tools. However, the functional complexity of the A. oryzae transcriptome has not yet been fully elucidated. Here, we applied direct high-throughput paired-end RNA sequencing (RNA-Seq) to the transcriptome of A. oryzae under four different culture conditions and confirmed most of the annotated genes. Moreover, with high resolution and sensitivity afforded by RNA-Seq, we were able to identify a substantial number of novel transcripts, new exons, untranslated regions, alternative upstream initiation codons (uATGs) and upstream open reading frames (uORFs), which serves a remarkable insight into the A. oryzae transcriptome. We also were able to assess the alternative mRNA isoforms in A. oryzae and found a large number of genes undergoing alternative splicing. Many genes or pathways that might involve in higher levels of protein production in solid-state culture than in liquid culture were identified by comparing gene expression levels between different cultures. Our analysis indicated that the transcriptome of A. oryzae was much more complex than previously anticipated and the results might provide a blueprint for further study of A. oryzae transcriptome.

overall_design: mRNA expression of Aspergillus oryzae in 4 different culture conditions was determined by method of RNA-Seq using short reads from high throughput sequencing technology.

first: Bin

last: Wang

first: Chao

first: Ying

last: Lin

first: Xiaoning

first: Mouming

last: Zhao

first: Yong

first: Minghui

last: He

last: Zhang

first: Li


title: ChIP-Seq analysis of ER binding sites in MCF7 breast cancer cells

first: Jindan

last: Yu

address: 303 E. Superior St.

department: Medicine - Hem/Onc

institute: Northwestern University

summary: Estrogen Receptor (ER) is a hormonal transcription factor that plays important roles in breast cancer. It functions primarily through binding to the regulatory regions of target genes containing the consensus ERE motifs.  In order to identify ER target genes and re-define the ERE motifs we performed ChIP-Seq analysis of ER in MCF7 breast cancer cell line.  Applying a novel computational algorithm named Hybrid Motif Sampler (HMS), specifically designed for TFBS motif discovery in ChIP-Seq data, we were able to detect an improved ERE motif and reveal intra-motif dependency especially in neighboring base pairs.

overall_design: MCF7 cells were grown in starving medium (RPMI with 5% FCS) for 3 days prior to the treatment with 10 nM β-estradiol or vehicle control for 45 minutes. ChIP was done using an anti-ER antibody in both the ethl-treated and the E2-treated cells.  ChIP-Seq sample prep and sequencing were done following the manufacture's protocol using the Genome Analyzer (Illumina). The read files were analyzed using ethl-treated as control for E2-treated, leading to one final peak file.

first: Arul

last: Chinnaiyan


title: High throughput sequencing of endogenous small RNAs from AGO pathway mutants

first: Craig

last: Mello

summary:
High-throughput pyrosequencing of endogenous small RNAs from >95% male enriched populations of alg-3(tm1155);alg-4(ok1041);fog-2(q71) and fog-2(q71) worms as well as purified spermatids from fem-3(q20) adult worms.
Gametogenesis is thermosensitive in numerous metazoa ranging from worms to man.  In C. elegans a variety of germ-line nuage- (P-granule) -associated RNA-binding proteins including the Piwi-clade Argonaute, PRG-1, have been implicated in temperature-dependent fertility.  Here, we describe the role of two AGO-class paralogs, alg-3 (T22B3.2) and alg-4 (ZK757.3) in promoting male fertility at elevated temperatures.  A rescuing GFP::alg-3 transgene is localized in P-granules beginning at the late pachytene stage of male gametogenesis. alg-3/4 double mutants lack a subgroup of small RNAs, named 26G-RNAs, which target and appear to down-regulate numerous spermatogenesis-expressed mRNAs. These findings add to a growing number of AGO pathways required for temperature-dependent fertility in C. elegans and support a model in which AGOs and their small RNA co-factors function to promote robustness in gene-expression networks.

overall_design: 3 samples examined. Small RNAs from alg-3(tm1155);alg-4(ok1041);fog-2(q71) males and fog-2(q71) males.   Small RNAs from spermatids isolated from ferm-3(q20) worms.

first: Colin

last: Conine


title: MicroRNAs of Bombyx mori identified by Solexa sequencing

city: Beibei

first: Qingyou

last: Xia

state: Chongqing

address: Tiansheng Road

department: College of Biotechnology

institute: Southwest University

summary: Background: MicroRNA (miRNA) and other small regulatory RNAs contribute to the modulation of a large number of cellular processes. We sequenced three total RNA libraries prepared from the whole body, and the anterior and posterior silk glands of Bombyx mori, with a view to expanding the repertoire of silkworm miRNAs and exploring transcriptional differences in miRNAs between segments of the silk gland. Results: With the aid of large-scale Solexa sequencing technology, we validated 244 unique miRNA genes, including 191 novel and 53 previously reported genes, corresponding to 309 loci in the silkworm genome. Interestingly, 24 unique miRNAs were widely conserved from invertebrates to vertebrates; 12 unique ones were limited to invertebrates and 33 were confined to insects; whereas the majority of the newly identified miRNAs were silkworm-specific. We identified 21 clusters and 42 paralogs of miRNAs in the silkworm genome. However, sequence tags showed that paralogs or clusters are not prerequisites for coordinated transcription and accumulation. The majority of silkworm-specific miRNAs are located in transposable elements, and display significant differences in abundance between the anterior and posterior silk glands. Conclusions: Conservative analysis revealed that miRNAs serve as phylogenetic markers and function in evolutionary signaling. The newly identified miRNAs greatly enriched the repertoire of insect miRNAs, and provide insights into miRNA evolution, biogenesis, and expression in insects. The differential expression of miRNAs in the anterior and posterior silk glands supports their involvement as new layers in the regulation of the silkworm silk gland.

overall_design: Sequencing three total RNA pools of the whole silkworm body from 5th-instar day-3 larvae, and anterior and posterior silkworm silk glands, using the latest sequencing Solexa technology

first: Shiping

last: Liu

first: Dong

last: Li

first: Qibin

first: Ping

first: Zhonghuai

last: Xiang


title: RNA-Seq of oral squamous cell carcinomas and matched normal tissues

city: Foster City

first: Brian

last: Tuch

state: CA

address: 850 Lincoln Center Dr.

institute: Life Technologies

summary: RNA-Seq was applied to oral squamous cell carcinomas and matched normal oral tissue to measure gene expression patterns and identify examples of allelic imbalance.

overall_design: Oral squamous cell carcinomas (OSCC) and matched normal tissue from 3 patients.

first: Rebecca

last: Laborde

first: David

middle: I

last: Smith


title: Hairpin RNA induces secondary small interfering RNA synthesis and silencing in trans in fission yeast

city: Edinburgh

first: Alastair

middle: Robert

last: Kerr

state: Midlothian

address: 2.21 Michael Swann Building, Kings Buildings, Mayfield Road

department: Wellcome Centre for Cell Biology

institute: University of Edinburgh

summary: We provide evidence of the generation of Rdp1-mediated secondary siRNAs in vivo in fission yeast. Secondly, we show that the presence of Ago1-associated siRNAs does not guarantee robust silencing.

overall_design: We obtained sequences from gel purified small RNAs of wt and rdp1delta fission yeast cells and FLAG-ago1 associated small RNAs.

first: Femke

last: Simmer

first: Alessia

last: Buscaino

first: Isabelle

last: Kos-Braun

first: Alexander

last: Kagansky

first: Abdelhalim

last: Boukaba

first: Takeshi

last: Urano

first: Robin

last: Allshire


title: Genome wide mapping of Jarid2 and Suz12 binding sites in mouse ES cells before and after Jarid2 depletion

status: Public on Jan 27 2010

city: Milano

first: Diego

last: Pasini

address: Via Adamello, 16

department: Experimental Oncology

country: Italy

institute: European Institute of Oncology

summary: We analyzed the overlap in genome wide binding sites between Jarid2 and Suz12 in mouse ES cells and find that Jarid2 and Suz12 peaks have an high degree (90%) of overlap. Moreover we analyzed the effect of Jarid2 down regulation on genome wide Suz12 binding sites and found that Loss of Jarid2 lead to the loss of 70% of Suz12 binding sites and to a 10 Fold reduction in intensity for 90% of Suz12 binding sites. Overall, these results demonstrate that Jarid2 plays an essential role for Suz12 (PRC2 complex) association to DNA.

overall_design: Examination of two different proteins in two different cell lines

first: Mads

last: Bak

first: Kristian

last: Helin


title: Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by Aid deficiency

status: Public on Jan 26 2010

city: Los Angeles

first: matteo

last: Pellegrini

address: 621 Charles Young Drive South

department: MCD Biology

institute: UCLA

type: Methylation profiling by high throughput sequencing

summary: Epigenetic reprogramming including demethylation of DNA occurs in mammalian primordial germ cells (PGCs) and in early embryos, and is important for the erasure of imprints and epimutations, and the return to pluripotency. The extent of this reprogramming and its molecular mechanisms are poorly understood. We previously showed that the cytidine deaminases Aid and Apobec1 can deaminate 5-methylcytosine in vitro and in E coli, and in the mouse are expressed in tissues in which demethylation occurs. Here we profiled DNA methylation throughout the genome by unbiased bisulfite Next Generation Sequencing (BS-Seq) in wildtype and Aid deficient PGCs at E13.5. Wildtype PGCs revealed dramatic genome-wide erasure of methylation to a level below that of methylation deficient (Np95-/-) ES cells, with female PGCs being less methylated than male ones. By contrast, Aid deficient PGCs were up to three times more methylated than wildtype ones; this substantial difference occurred throughout the genome, with introns, intergenic regions and transposons being relatively more methylated than exons. Relative hypermethylation in Aid deficient PGCs was confirmed by analysis of individual loci in the genome. Our results reveal that erasure of DNA methylation in the germ line is a global process, hence limiting the potential for transgenerational epigenetic inheritance. Aid deficiency interferes with genome-wide erasure of DNA methylation patterns, suggesting that Aid has a critical function in epigenetic reprogramming and potentially in restricting the inheritance of epimutations in mammals.

overall_design: Comparison of methylation in wild-type and Aid deficient mouse tissues

first: Christian

last: Popp

first: Wendy

last: Dean

first: Suhua

last: Feng

first: Shawn

last: Cokus

first: Simon

last: Andrews

first: Matteo

first: Steven

last: Jacobsen

first: Wolf

last: Reik


title: A map of open chromatin in human pancreatic islets

status: Public on Jan 31 2010

city: San Diego

first: Kyle

middle: Jeffrie

last: Gaulton

address: 9500 Gilman Drive

department: Pediatrics

institute: UCSD

type: Genome binding/occupancy profiling by genome tiling array

summary:
High-throughput sequencing of genomic regions isolated using FAIRE (Formaldehyde-assisted isolation of regulatory elements) from three purified pancreatic islet samples

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:
Identification of nucleosome-depleted genomic regions in three human pancreatic islet samples

This work was carried out in the laboratories of Jason Lieb and Jorge Ferrer, and was supported in part by a subcontract to J. Lieb from Greg Crawford's ENCODE grant.

first: Takao

last: Nammo

first: Lorenzo

last: Pasquali

first: Karen

last: Mohlke

first: Jason

last: Lieb

first: Jorge

last: Ferrer


title: mRNA-Seq of head tissue from Drosophila pseudoobscura

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

summary:
We sequenced mRNA from head tissue of females and male of Drosophila pseudobscura to identify genes differentially expressed between the sexes and sex-specific alternative splicing events.

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: Comparison of expression profiles in female and male head tissue from D. pseudobscura

first: John

middle: H

last: Malone


title: High-throughput sequencing of small RNAs in Miscanthus x giganteus

city: Udine

first: Emanuele

last: De Paoli

state: UDINE

address: via delle Scienze 206

department: Agricultural, Food, Environmental and Animal Sciences

institute: University of Udine

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

overall_design: Small RNA libraries were derived from leaves, flowers and rhizomes of Miscanthus x giganteus. Each tissue represented a mixture of developmental stages, with a bias towards those from early, actively differentiating cells.  For rhizomes, the apical tip portion was collected. Total RNA was isolated using the Plant RNA Purification Reagent (Invitrogen) and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Steven Moose for providing the plant material and Kan Nobuta for assistance with the computational methods.

last: DePaoli

first: Monica

last: Accerbi

first: Pamela

last: Green

first: Blake

last: Meyers


title: Genome-wide mapping of Nr5a2 in mouse embryonic stem cells

status: Public on Jan 22 2010

city: Singapore

first: Mikael

last: Huss

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

summary:
Nr5a2 (also known as liver receptor homolog-1, Lrh-1) has been shown to bind both the proximal enhancer and proximal promoter regions of Pou5f1 and regulate Pou5f1 in the epiblast stage of mouse embryonic development (Gu et al., 2005). Nr5a2-null embryos display a loss of Oct4 expression in the epiblasts (Gu et al., 2005) and die between E6.5 and E7.5 (Gu et al., 2005; Pare et al., 2004). To identify the targets of Nr5a2, we generated a stable ES cell-line that expresses HA-tagged Nr5a2. Anti-HA antibody was used to immunoprecipitate HA-Nr5a2 for ChIP-seq analysis.

Keywords: Transcription factor binding sites

overall_design: To identify the binding sites of Nr5a2, we generated a stable ES cell-line that expresses HA-tagged Nr5a2. Anti-HA antibody was used to immunoprecipitate HA-Nr5a2.

first: D

last: Heng

first: H

last: Ng


title: U87MG Decoded: The Genomic Sequence of a Cytogenetically Aberrant Human Cancer Cell Line

status: Public on Jan 25 2010

first: Stanley

last: Nelson

address: 695 Young Dr S

department: Human Genetics

type: Genome variation profiling by high throughput sequencing

summary: U87MG is a commonly studied grade IV glioma cell line that has been analyzed in at least 1,700 publications over four decades. In order to comprehensively characterize the genome of this cell line and to serve as a model of broad cancer genome sequencing, we have generated greater than 30x genomic sequence coverage using a novel 50-base mate paired strategy with a 1.4kb mean insert library. A total of 1,014,984,286 mate-end and 120,691,623 single-end two-base encoded reads were generated from five slides. All data were aligned using a custom designed tool called BFAST, allowing optimal color space read alignment and accurate identification of DNA variants. The aligned sequence reads and mate pair information identified 35 interchromosomal translocation events, 1,315 structural variations (>100bp), 191,743 small (<21bp) insertions and deletions (indels), and 2,384,470 single nucleotide variations (SNVs). Among these observations, the known homozygous mutation in PTEN was robustly identified, and genes involved in cell adhesion were overrepresented in the mutated gene list. Data were compared to 219,187 heterozygous single nucleotide polymorphisms assayed by Illumina 1M Duo genotyping array to assess accuracy: 93.83% of all SNPs were reliably detected at filtering thresholds that yield greater than 99.99% sequence accuracy. Protein coding sequences were disrupted predominantly in this cancer cell line due to small indels, large deletions and translocations. In total, 512 genes were homozygously mutated, including 154 by SNVs, 178 by small indels, 145 by large microdeletions and 35 by interchromosomal translocations to reveal a highly mutated cell line genome. Of the small homozygously mutated variants, 8 SNVs and 99 indels were novel events not present in dbSNP. These data demonstrate that routine generation of broad cancer genome sequence is possible outside of genome centers. The sequence analysis of U87MG provides an unparalleled level of mutational resolution compared to any cell line to date.

overall_design: Whole genome sequencing of the U87MG brain cancer cell line using the AB SOLiD3 sequencer and genotyping using the Illumina Human1M-Duov3 DNA Analysis BeadChip

first: Michael

last: Clark


title: CNV Kc-167 Cells

status: Public on Jan 21 2010

first: DCC

last: modENCODE

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

institute: Ontario Institute for Cancer Research

summary:
modENCODE_submission_2552
This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: Analysis of copy number variation across modENCODE Drosophila cell line by high throughput sequencing.  We observe numerous copy number variations for the different cell lines, with each cell line having a distinct ploidy signature.

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

Keywords: deep sequencing analysis

overall_design: EXPERIMENT TYPE: deep sequencing analysis. BIOLOGICAL SOURCE: Cell Line: Kc167; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Genotype: se/e; Sex: Female;  EXPERIMENTAL FACTORS: Cell Line Kc167

first: David

last: MacAlpine

first: Sara

last: Powell

first: Matthew

last: Eaton

first: Prinz

last: Joseph


title: CNV ML-DmBG3-c2 Cells

summary:
modENCODE_submission_2553
This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: Analysis of copy number variation across modENCODE Drosophila cell line by high throughput sequencing.  We observe numerous copy number variations for the different cell lines, with each cell line having a distinct ploidy signature.

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

Keywords: deep sequencing analysis

overall_design: EXPERIMENT TYPE: deep sequencing analysis. BIOLOGICAL SOURCE: Cell Line: ML-DmBG3-c2; Tissue: CNS-derived cell-line; Developmental Stage: third instar larval stage; Genotype: y v f mal; Sex: Unknown;  EXPERIMENTAL FACTORS: Cell Line ML-DmBG3-c2


title: Virus-derived siRNAs in Arabidopsis thaliana

status: Public on Jan 20 2010

city: Riverside

first: Qingfa

last: Wu

address: 900 University Ave

institute: UC Riverside

summary: We investigated the role of A. thaliana RDRs in the RNAi-mediated viral immunity by using a mutant of cucumber mosaic virus (CMV) that does not express the VSR protein 2b. CMV contains three positive-strand genomic RNAs and the 2b protein encoded by RNA2 is essential for infection by suppressing antiviral silencing initiated by either DCL4 or DCL2. Our results demonstrate an essential role for the amplification of viral siRNAs by either RDR1 or RDR6 in antiviral silencing. Further analyses, including Illumina sequencing of more than 3.5 million viral siRNAs, indicated target specificity of the two antiviral RDRs.

sample_organism:
Arabidopsis thaliana
Cucumber mosaic virus (strain FNY)

overall_design: Examination of the viral siRNAs of CMV in the wild-type and mutants of A. thaliana

first: Xianbing

last: Wang

first: Shou-wei

last: Ding


title: Genome-wide localization of the RNA polymerase III transcription machinery in human cells

status: Public on Feb 11 2010

city: Lausanne

first: Nicolo

last: Riggi

state: VD

address: Bugnon 25

department: Département de Pathologie Expérimentale

institute: CHUV

summary: To characterize the pol III transcriptome in actively growing human cells, we used MR90hTeIrt lung fibroblasts, which are immortal but not transformed, with an intact Rb pathway.  After formaldehyde cross-linking, chromatin was extracted and submitted to immunoprecipitation.  To identify actively transcribed RNAP-III transcription units, we used antibodies directed against the RPC4 subunit of RNAP-III.  To identify promoter regions, we used antibodies directed against Bdp1, which is part of both Brf1-TFIIIB and Brf2-TFIIIB, and thus should mark all types of active RNAP-III promoters.  Antibodies directed against Brf1 were used to mark type 1 and 2 promoters.  For type 3 promoters, we engineered an IMR90hTert cell line expressing the SNAPc subunit SNAP45 tagged at its C-terminal end with the biotin acceptor domain as well as the biotin ligase BirA and performed “chromatin affinity purification” (ChAP) with streptavidin beads. In each case, the precipitated material was then processed for deep sequencing.

overall_design: ChIP-enriched DNA  or ChAP-enriched DNA from MR90hTeIrt cells were analyzed by Illumina high-throughput sequencing. This analysis includes ChIP data done with antibodies against : RPC4, Bfr1, Bdp1 and SNAP45. Two lanes were run for RPC4, Brf1 and SNAP45, and three for Bdp1. One lane was run with Input DNA for control.

first: Nouria

last: Hernandez

first: Donatella

last: Canella

first: Jaime

last: Reina

first: Pascal

last: Cousin

first: Viviane

last: Praz


title: CNV S2-DRSC Cells

summary:
modENCODE_submission_2551
This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: Analysis of copy number variation across modENCODE Drosophila cell line by high throughput sequencing.  We observe numerous copy number variations for the different cell lines, with each cell line having a distinct ploidy signature.

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

Keywords: deep sequencing analysis

overall_design: EXPERIMENT TYPE: deep sequencing analysis. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male;  EXPERIMENTAL FACTORS: Cell Line S2-DRSC


title: Dissecting the unique role of the retinoblastoma tumor suppressor during cellular senescence

status: Public on Jan 15 2010

city: Cold Spring Harbor

first: Agustin

last: Chicas

address: One Bungtown Road

institute: Memorial Sloan Kettering

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

overall_design: Refer to individual Series


title: Expression in Aneuploid Drosophila S2 Cells

status: Public on Jan 11 2010

first: Brian

last: Oliver

type: Genome binding/occupancy profiling by array

summary:
Chromosomal and segmental aneuploidies are usually lethal or common features of cancer cells and variety of disease, but little is known about how copy number relates to gene expression. Drosophila males have a single X chromosome and two sets of autosomes, but X chromosome and autosome transcripts are equally abundant.  This 2-fold increase in X chromosome gene expression requires a dosage compensation complex (MSL) that acetylates histone 4 at lysine 16 (H4AcK16).  To determine the contribution of general buffering and MSL to X chromosome dosage compensation, we analyzed genome-wide copy number, expression and histone modification pattern in male Drosophila S2 cells with and without MSL.

Keywords: Gene Regulation Study, genomic analyses

overall_design: RNA-seq and microarray were performed in Drosophila non-treated or RNAi treated S2 cells. Two biological replicates were used for expression profile. DNA-seq and CGH were performed (CGH data forthcoming) to check the copy number variation in S2 cells. Chromatin immunoprecipitations were performed in Drosophila non-treated or RNAi treated S2 cells with different histone modification antibodies. At least three biological replicates were performed for each antibody and treatment.

first: Yu

last: Zhang


title: The TDRD9-MIWI2 complex is essential for piRNA-mediated retrotransposon silencing in the mouse male germline

status: Public on Jan 06 2010

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

institute: University of Geneva

summary: We identify small RNA partners of Mili from 14 dpp testes of Tdrd9-/- and Tdrd9+/- mice. Two technical replicates of the same library are indicated as replicate 1 and 2.

overall_design: Examination of differences in Mili-associated RNAs in 14 dpp testes of Tdrd9-/- and Tdrd9+/- mice

first: Michael

last: Reuter

first: Alexander

last: Stark


title: Xenopus egg small RNA associated with Y12 antibody

status: Public on Jan 04 2010

city: New York

first: Nicolas

last: Robine

address: 1275 York Avenue, Box 252

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

summary: We examined in Xenopus tropicalis eggs piRNAs that are associated with Y12 antibody, which binds symmetrically methylated arginines that are present on diverse Piwi proteins. The goal of this experiment is to more deeply characterize the piRNA pool from adult Xenopus extracts, using the Illumina platform.

overall_design: Sequencing of a cDNA library from small RNAs from the Y12 immunoprecipitate

first: Nelson

last: Lau

first: Eric

last: Lai


title: Sex-dependent and -independent X-chromosome histone modifications in Drosophila melanogaster

summary: Drosophila X chromosomes are subject to dosage compensation in males and are known to have a specialized chromatin structure in the male soma.  We are interested in how specific chromatin structure change contributes to X chromosome hyperactivity and dosage compensation. We have conducted a global analysis of localize two dosage compensation complex dependent histone marks H4AcK16 and H3PS10 and one dosage compensation complex independent histone mark H3diMeK4 in the genome, especially on X chromosome by ChIP-chip approach in both male and female adult flies. We also probed general genomewide chromatin structure by deep DNA sequencing of sheared ChIP input DNA from male and female adult flies.

overall_design:
Chromatin immunoprecipitations were performed in 5-7 day aged adult male and female flies with three histone modification antibodies. ChIP enriched DNA and input DNA was labeled by Cy3 or Cy5 dye separately and hybridized simultaneously to the Drosophila FlyGEM arrays. At least two biological replicates were performed for each antibody and sex.
DNA-seq (NIDDK-Drosophila-Illumina-DNASeq) were performed on ChIP-input sheared DNA to check the general chromatin structure of different chromosome.


title: Listeria monocytogenes Transcriptome with RNA-Seq

status: Public on Jan 05 2010

city: Ithaca

first: Lalit

last: Ponnala

address: 616 Rhodes Hall

institute: Cornell University

summary:
The stationary phase stress response transcriptome of the human bacterial pathogen Listeria monocytogenes was defined using RNA sequencing (RNA-Seq) with the Illumina Genome Analyzer.  Specifically, bacterial transcriptomes were compared between stationary phase cells of L. monocytogenes 10403S and an otherwise isogenic DsigB mutant, which does not express the alternative sigma factor σB, a major regulator of genes contributing to stress response.

Keywords: Transcriptome and differential expression analyses

overall_design: a laboratory strain, 10403S and its otherwise isogenic mutant lacking sigB were analyzed. Two replicates of each strain were analyzed for a total of 4 runs

first: Haley

first: Renato

last: Orsi

first: Uri

last: Keich

first: Wei

last: Wnag

first: Qi

last: Sun

first: Samuel

middle: W

last: Cartinhour

first: Melanie

last: Filiatrault

first: Martin

last: Wiedmann

first: Kathryn

last: Boor


title: Analysis of interleukin-21-induced Prdm1 gene regulation reveals functional cooperation of STAT3 and IRF4 TFs

status: Public on Jan 08 2010

first: Warren

last: Leonard

address: 10 Center Dr

institute: NHLBI/NIH

summary: Interleukin-21 (IL-21) is a pleiotropic cytokine that induces expression of transcription factor BLIMP1 (encoded by Prdm1), which regulates plasma cell differentiation and T cell homeostasis. We identified an IL-21 response element downstream of Prdm1 that binds the transcription factors STAT3 and IRF4, which are required for optimal Prdm1 expression. Genome-wide ChIP-Seq mapping of STAT3- and IRF4-binding sites showed that most regions with IL-21-induced STAT3 binding also bound IRF4 in vivo, and furthermore, revealed that the noncanonical TTCnnnTAA GAS motif critical in Prdm1 was broadly used for STAT3 binding. Comparing genome-wide expression array data to binding sites revealed that most IL-21-regulated genes were associated with combined STAT3-IRF4 sites rather than pure STAT3 sites. Correspondingly, ChIP-Seq analysis of Irf4_/_ T cells showed greatly diminished STAT3 binding after IL-21 treatment, and Irf4_/_ mice showed impaired IL- 21-induced Tfh cell differentiation in vivo. These results reveal broad cooperative gene regulation by STAT3 and IRF4.

overall_design:
Affymetrix expression data: Prepare CD4+ T cells from spleen. CD4+ T cells were preactivated, rested, and treated with IL-21 for 1, 6, and 24 hours.
ChIP-seq data: Profiling of IRF4 and Stat3 binding with and without IL-21 stimulation in wild type and IRF4 KO mice.

first: Hyokjoon

last: Kwon

first: Danielle

last: Thierry-Mieg

first: Jean

first: Jangsuk

last: Oh


title: Global Epigenetic and Transcriptional Trends among Two Rice Subspecies and Their Reciprocal Hybrids.

city: New Haven

first: guangming

last: he

address: 165, prospect st.

department: MCDB

institute: Yale University

summary: The behavior of transcriptomes and epigenomes in hybrids of heterotic parents is of fundamental interest. Here we report highly integrated maps of the epigenome, mRNA and small RNA transcriptomes of two rice subspecies and their reciprocal hybrids. We found that gene activity was correlated with DNA methylation and both active and repressive histone modifications in transcribed regions. Differential epigenetic modifications correlated with changes in transcript levels among hybrids and parental lines. Distinct patterns in gene expression and epigenetic modifications in reciprocal hybrids were observed. Through analyses of single nucleotide polymorphisms from our sequence data, we observed a high correlation of allelic bias of epigenetic modifications or gene expression in reciprocal hybrids with their differences in the parental lines. The abundance of distinct small RNA size classes differed between the parents and more small RNAs were down-regulated than up-regulated in the reciprocal hybrids. Together, our data reveals a comprehensive overview of transcriptional and epigenetic trends in heterotic rice crosses, and provides a very useful resource for the rice community.

overall_design: Genome-wide integrated mapping of mRNA transcripts, DNA methylation and three select histone modifications (H3K4me3, H3K9ac and H3K27me3), using shoots of four-leaf stage seedlings of two rice subspecies (Oryza sativa L. ssp. japonica cv. Nipponbare and Oryza sativa L. ssp. indica cv. 93-11) and their reciprocal hybrids (Nipponbare/93-11 and 93-11/Nipponbare).

first: Guangming

last: He

first: Xingwang

last: Deng


title: Jarid2 and PRC2, Partner in Regulating Gene Expression

status: Public on Jan 01 2010

city: boston

first: Manching

last: Ku

address: 185 Cambridge St. CPZN-8400

institute: MGH

summary: The Polycomb Group proteins foster gene repression profiles required for proper development and unimpaired adulthood, and comprise the components of the PRC2 complex including the histone H3 lysine 27 (H3K27) methyltransferase Ezh2. How mammalian PRC2 accesses chromatin is unclear. We find that Jarid2 associates with PRC2 and stimulates its enzymatic activity in vitro.  Jarid2 contains a Jumonji C domain, but is devoid of detectable histone demethylase activity. Instead, its artificial recruitment to a promoter in vivo resulted in co-recruitment of PRC2 with resultant increased levels of H3K27me2/3. Jarid2 co-localizes with Ezh2 and MTF2, a homologue of Drosophila Pcl, at endogenous genes in ES cells. Jarid2 can itself bind DNA and its recruitment in ES cells is interdependent with that of PRC2 as Jarid2 knockdown reduced PRC2 at its target promoters, and ES cells devoid of the PRC2 component EED are deficient in Jarid2 promoter access. In addition to the well-documented defects in embryonic viability upon down-regulation of Jarid2, ES cell differentiation is impaired, as is Oct4 silencing.

overall_design: Examination of two factors  in ES cells

first: Bradley

last: Bernstein

first: Danny

last: Reinberg


title: Mili-IP, Miwi-IP, and total RNA from mouse adult testis

first: Nicolas

last: Robine

summary: We deep-sequenced small RNAs after immunoprecipitation of Mili or Miwi, as well as total small RNA from adult mouse testis.  The goal of this experiment is to more deeply characterize the piRNA pool from adult mouse testes, using the Illumina platform.

overall_design: Comparison of 2 IP libraries with a non-IP library

first: Nelson

last: Lau

first: Eric

last: Lai


title: Genome-wide analysis of RB and p130 binding in human diploid fibroblasts

first: Agustin

last: Chicas

summary: The action of RB as a tumor suppressor has been difficult to define, in part, due to the redundancy of the related proteins p107 and p130. By coupling advanced RNAi technology with a genome wide analysis of gene expression and RB chromatin binding, we identified a unique and specific activity of RB in repressing DNA replication as cells exit the cell cycle into senescence, a tumor suppressive program.

overall_design: Binding of RB was examined in growing, quiescent, senescent or senescent cells lackign RB. Binding of p130 was examined in quiescent or senescent cells in the presence or absence of RB.  Libraries were prapered from DNA co-precipiated with RB or p130 specific antibodies or from  mock (beads-only) immunoprecipiates.

first: Scott

last: Lowe

first: Xiaowo

last: Wang


title: Melanoma short-term cultures and cell lines: expression profiling and CNV analyses

status: Public on Feb 01 2010

city: Cambridge

first: Michael

last: Berger

address: 7 Cambridge Center

institute: The Broad Instititute


title: Degradome sequencing reveals endogenous small RNA targets in rice (Oryza sativa L. ssp. indica)

city: Beijing

first: xiaofeng

last: cao

address: West Lincui Road, Chaoyang District

department: State Key Laboratory of Plant Genomics

institute: Institute of Genetics and Developmental Biology

summary: MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) regulate gene expression in eukaryotes. Plant miRNAs modulate their targets mainly via messenger RNA (mRNA) cleavage. Small RNA targets have been extensively investigated in Arabidopsis using computational prediction, experimental validation, and degradome sequencing. However, small RNA targets are largely unknown in rice (Oryza sativa). Here, we report global identification of small RNA targets using high throughput degradome sequencing in the rice indica cultivar 93-11 (Oryza sativa L. ssp. indica). 177 transcripts targeted by total of 87 unique miRNAs were identified. Of targets for the conserved miRNAs between Arabidopsis and rice, transcription factors comprise around 70% (58 in 82), indicating that these miRNAs act as masters of gene regulatory nodes in rice. In contrast, non-conserved miRNAs targeted diverse genes which provide more complex regulatory networks. In addition, 5 AUXIN RESPONSE FACTORS (ARF) cleaved by the TAS3 derived ta-siRNAs were also detected. A total of 40 sRNA targets were further validated via RNA ligase-mediated 5’ rapid amplification of cDNA ends (RLM 5’-RACE). Our degradome results present a detailed sRNA-target interaction atlas, which provides a guide for the study of the roles of sRNAs and their targets in rice.

overall_design: The degradome sequence of Young inflorescences from Oryza sativa L. ssp. indica (93-11) was sequenced

first: Ming

last: Zhou

first: Lianfeng

last: Gu

first: Pingchuan

last: Li

first: Xianwei

last: Song

first: Liya

last: Wei

first: Zhiyu

last: Chen

first: Xiaofeng

last: Cao


title: Genome-wide maps of chromatin state in staged Drosophila embryos and cell lines.

city: Chicago

first: Kevin

middle: P.

last: White

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 ChIP-seq data generated on Solexa Genome Analyzer for several Transcription Factors and Chromatin associated Proteins. This dataset is called February_1st_datafreeze and is part of the regular datafreezes we produce for the modENCODE project.

Keywords: Epigenetics

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

overall_design: For each experiment, at least 2 replicates of ChIP have been performed (except Caudal in Adult Female and E4-8h) and compared to an Input sample(s). The factors analyzed in this freeze are: CTCF in S2 cells, Caudal in embryos 0-4h, embryos 4-8h, L3 larvae and Adult Female,  EcR in White Pre-Pupae (10 to 11 hours and 30 to 33 hours) and HDAC1, HDAC3, HDAC6, HDAC4a and HDAC11 in Embryos 0-12h. ChIP samples have been sequenced on the Solexa Genome Analyser  (36 bp reads) following the standard Illumina protocol.

last: Negre

first: Nick

middle: A

last: Bild

middle: P


title: Genome-wide mapping of RNA Pol II binding site (GM12878)

status: Public on Dec 31 2009

first: Flora

last: Vaccarino

address: 230 South Frontage Road

department: Child Study Center

summary:
We report the results of chromatin immunoprecipitation following by high-thoughput sequencing (ChIP-Seq) using the GA II platform from Illumina for the human  RNA Polymerase II in GM12878 cells. We have also generated a sequenced input DNA datasets for GM12878 cells.

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: Map binding sites of RNA Polymerase II in the genome of GM12878 cells. The GM12878 input data has been deposited in GEO as GSM487430.

first: Debasish

last: Raha

last: Snyder


title: Genome-wide mapping of RNA Pol III binding site (GM12878)

summary:
We report the results of chromatin immunoprecipitation following by high-thoughput sequencing (ChIP-Seq) using the GA II platform from Illumina for the human  RNA Polymerase III in GM12878 cells. We have also generated a sequenced input DNA datasets for GM12878 cells.

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: Map binding sites of RNA Polymerase III in the genome of GM12878 cells.


title: Genome-wide mapping of Jun binding site (K562)

summary:
Proto-oncogene c-jun is a leucine-zipper containing transcription factor which has a DNA binding domain and a transactivation domain. Jun dimerizes with another transcription factor Fos to form AP1 transcription factor. The AP-1 complex has been implicated in transformation and progression of cancer.

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: Map binding sites of transcription factor Jun in the genome of K562 cells. The K562 input data has been deposited in GEO as GSM325934.


title: Genome-wide mapping of RNA Pol III binding site (K562)

summary:
We report the results of chromatin immunoprecipitation following by high-thoughput tag sequencing (ChIP-Seq) using the GA II platform from Illumina for the human  RNA Polymerase III in K562 cells. We have also generated a sequenced input DNA datasets for K562 cells.

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: Map binding sites of RNA Polymerase III in the genome of K562 cells. The K562 input data has been deposited in GEO as GSM325934.


title: Genome-wide mapping of Myc binding site (K562)

summary:
Proto-oncogene c-myc encodes a bHLH leucine-zipper containing transcription factor which has a DNA binding domain and a transactivation domain. Myc can dimerize with other factors like Max, Mad, Mnt and Miz and can influence transcription of genes. The c-myc oncogene contributes to the genesis of a wide variety of human tumors. A higher than normal level of c-myc gene expression has been observed in 50-80% of colon and breast cancers and a large proportion of human mortality from cancer is caused by abnormal expression of c-myc.

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: Map binding sites of transcription factor Myc in the genome of K562 cells. The K562 input data has been deposited in GEO as GSM325934.


title: Genome-wide mapping of Fos binding site (K562)

summary:
Proto-oncogene c-Fos is a leucine-zipper containing transcription factor which has a DNA binding domain and a transactivation domain. Fos dimerizes with another transcription factor Jun to form AP1 transcription factor. The AP-1 complex has been implicated in transformation and progression of cancer.

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: Map binding sites of transcription factor Fos in the genome of K562 cells. The K562 input data has been deposited in GEO as GSM325934.


title: Changes in expression of small non-coding RNAs/microRNAs during aging in C. elegans

first: Frank

last: Slack

address: 266 Whitney Ave

summary:
We report a significant number of miRNAs and other non-coding small RNAs show dramatic changes in expression during aging in C. elegans. RNAs were prepared from four diffrent timepoints during adulthood of C. elegans hermaphrodites, Day 0, 5, 8 and 12 post-L4 molt, and used for making cDNA libraries for small RNAs. Each library was sequenced using recent advances in high-throughput sequencing technology, Solexa. This study should lead to a better understanding of the aging process and age-related diseases.

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: Examination of small RNA expression in four timepoints during adulthood of C. elegans hermaphrodites (spe-9 (hc88), cultured at 23dC), Day 0, 5, 8 and 12 post L4-molt.

first: Masaomi

last: Kato


title: The Tasmanian devil transcriptome reveals Schwann cell origins of a clonally transmissible cancer (small RNA sequencing)

first: Pouya

last: Kheradpour

address: 32 Vassar St 32-G822

institute: Massachusetts Institute of Technology

summary: The Tasmanian devil, a marsupial carnivore, is endangered due to the emergence of a clonally transmissible cancer known as Devil Facial Tumor Disease (DFTD). This fatal cancer is clonally derived and is an allograft transmitted between devils by biting. We performed a large-scale genetic analysis of DFTD with microsatellite genotyping, mitochondrial genome analysis, as well as deep sequencing of the DFTD transcriptome and miRNAs. These studies confirm that DFTD is a monophyletic clonally transmissible tumor, and suggest that the disease is of Schwann cell origin. On the basis of these results we have generated a diagnostic marker for DFTD, and identify a suite of genes of relevance to DFTD pathology and transmission. We provide a genomic dataset for the Tasmanian devil, which is applicable to cancer diagnosis, disease evolution and conservation biology. This submission contains only small RNA sequence data from this study.

overall_design: Small RNA (18 - 24 nt) sequences from 15 Tasmanian devil (Sarcophilus harrisii) tissue samples

first: Elizabeth

last: Murchison

first: Gregory

last: Hannon


title: High-throughput sequencing of small RNAs in Zea mays (maize)

first: Emanuele

last: De Paoli

address: via delle Scienze 206

summary: Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from different maize tissues (including leaves, ears and tassels) collected from wild-type plants of the B73 variety. The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the maize genome under study.

overall_design: Small RNA libraries were derived from leaves, ears and tassels of maize variety B73 (wild-type). Plants were grown in a flood irrigated plot at the University of Arizona (Tucson, AZ, USA) in 2007 and organs were pooled from several plants for each library. Young leaves were collected from 6-weeks-old seedlings. Post-meiotic immature ears were harvested from 10- and 11-week old plants while pre-meiotic tassels were collected from 8-week old plants. Total RNA was isolated using the Plant RNA Purification Reagent (Invitrogen) and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Lyudmila Sidorenko and Vicki Chandler for providing the plant material and Kan Nobuta for assistance with the computational methods.

first: Monica

last: Accerbi

first: Pamela

last: Green

first: Blake

middle: C

last: Meyers


title: Close Association of RNA Polymerase II and Many Transcription Factors With Pol III Genes

summary:
Transcription of the eukaryotic genomes is carried out by three distinct RNA polymerases I, II and III whereby each polymerase is thought to independently transcribe a distinct set of genes. To investigate a possible relationship of RNA polymerases II and III we mapped their in vivo binding sites throughout the human genome using ChIP Seq in two different cell lines, GM12878 and K562 cells. Pol III was found to bind near many known genes as well as several novel genes. RNA-Seq studies indicate that majority of the genes are expressed although a subset are not suggestive of stalling by RNA polymerase III. Pol II was found to bind near many known Pol III genes, including tRNA, U6, HVG, hY and 7SK and novel Pol III genes. Similarly, in vivo binding studies also reveal that a number of transcription factors normally associated with Pol II transcription, including c-Fos, c-Jun and c-Myc, also tightly associate with most Pol III transcribed genes. Inhibition of Pol II activity using ?-amanitin reduced expression of a number of Pol III genes (e.g. U6, hY, HVG), suggesting that Pol II plays an important role in regulating their transcription. These results indicate that, contrary to previous expectations, polymerases can often work with one another to globally coordinate gene expression.

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: GSE19545
SuperSeries of: GSE19546
SuperSeries of: GSE19547
SuperSeries of: GSE19548
SuperSeries of: GSE19549
SuperSeries of: GSE19550

overall_design: Refer to individual Series.


title: Jarid2/Jumonji coordinates control of PRC2 enzymatic activity and target gene occupancy in pluripotent cells

status: Public on Dec 24 2009

city: Stanford

first: Anton

last: Valouev

address: 300 Pasteur Dr.

department: Pathology

institute: Stanford University

summary: We report on mechanism of interaction between PRC2 complex and Jarid2 and their role in pluripotent cells

overall_design: Examination of PRC2 genomic localization by analysis of Jarid2, Ezh2, Suz12 and Jarid1a occupancy

first: Joanna

last: Wysocka


title: DNA specificity determinants associate with distinct transcription factor functions

status: Public on Dec 18 2009

city: Bloomington

first: Peter

last: Hollenhorst

state: IN

address: 1001 E Third St, Jordan Hall 104

institute: Indiana University

summary: To elucidate how genomic sequences build transcriptional control networks we need to understand the connection between DNA sequence and transcription factor binding and function.  Binding predictions based solely on consensus predictions are limited because a single factor can use degenerate sequence motifs and related transcription factors often prefer identical sequences.  The ETS family transcription factor, ETS1, exemplifies these challenges.  Unexpected, redundant occupancy of ETS1 and other ETS proteins is observed at promoters of housekeeping genes in T cells due to common sequence preferences and the presence of strong consensus motifs.  However, ETS1 exhibits a specific function in T cell activation, thus unique transcriptional targets are predicted.  To uncover the sequence motifs that mediate specific functions of ETS1, chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) identified both promoter and enhancer binding events in Jurkat T cells.  A comparison with DNase I sensitivity both validated the dataset and improved accuracy.  Redundant occupancy of ETS1 with the ETS protein GABPA occurred primarily in promoters of housekeeping genes, whereas ETS1 specific occupancy occurred in the enhancers of T-cell specific genes.  Two routes to ETS1 specificity were identified: an intrinsic preference of ETS1 for a variant of the ETS family consensus sequence and the presence of a composite sequence that can support cooperative binding with a RUNX transcription factor.  Genome-wide occupancy of RUNX factors corroborated the importance of this partnership.  Furthermore, genome-wide occupancy of co-activator CBP indicated tight co-localization with ETS1 at specific enhancers, but not redundant promoters.  The distinct sequences associated with redundant versus specific ETS1 occupancy were predictive of promoter or enhancer location and the ontology of nearby genes.  These findings demonstrate that diversity of binding motifs may enable variable transcription factor function at different genomic sites.

overall_design: Each ChIP sample was pooled from three independent immunoprecipitation experiments

first: Katherine

middle: J

last: Chandler

first: Rachel

last: Poulsen

first: W

last: Johnson

first: Nancy

last: Speck

first: Barbara

last: Graves


title: Pyrococcus furiosus psiRNAs

status: Public on Dec 28 2009

city: Farmington

first: Brenton

middle: R

last: Graveley

address: 400 Farmington Avenue

department: Genetics and Genome Sciences

institute: University of Connecticut Health Center

summary:
Small RNA Sequencing from Pyrococcus furiosus

Keywords: Small RNA Analysis

overall_design: Analysis of Small RNA from one sample of Pyrococcus furiosus

first: Michael

last: Duff

first: Sara

last: Olson

last: Terns

first: Rebecca

first: Caryn

last: Hale

first: Peng

last: Zhao

first: Lance

last: Wells


title: The integrative analysis of microRNA and mRNA expression in mouse uterus under delayed implantation and activation

status: Public on Dec 15 2009

city: Shantou

first: Zeng-Ming

last: Yang

address: 263 Daxue Road

department: Biology

institute: Shantou University

summary: This study was to elucidate the molecular mechanisms on delayed implantation in a global perspective through the combination of global microRNAs (miRNAs) and mRNA expression analysis in mouse uterus through Solexa sequencing.

overall_design: Examination of m/miRNA expression in mouse uterus.

first: Zengming

first: Jilong

last: Liu

first: Renwei

last: Su

first: Wei

last: Lei


title: PML-RARa/RXR alters the epigenetic landscape in Acute Promyelocytic Leukemia

status: Public on Dec 17 2009

city: Nijmegen

last: Stunnenberg

address: Geert Grooteplein 28

department: Department of Molecular Biology (274)

institute: Radboud University

summary: Many different molecular mechanisms have been suggested to be associated with PML-RAR dependent transformation of haematopoietic progenitors. Here, we investigated the role of PML-RAR and RXR in the organization of epigenetic structures at a genome-wide level. We identified 2722 high confidence PML-RAR binding sites in the leukemic model cell line NB4 and found PML-RAR colocalization with RXR to the vast majority of these binding regions. Importantly, these results could be corroborated and extended in primary blast cells of two APL patients. Through genome-wide epigenetic studies we show that treatment with pharmacological doses of all-trans retinoic acid ATRA induces global alterations in active H3 acetylation and repressive H3K27me3, H3K9me3 and DNA methylation chromatin modifications. However at the PML-RAR/RXR binding sites, ATRA only induces changes in H3 acetylation. These H3 acetylation alterations triggered by the loss of PML-RAR/RXR binding affect H3 acetylation and RNA polymerase II occupancy at nearby genes. Our results suggest that PML-RAR/RXR functions as a local chromatin modulator and that specific recruitment of histone deacetylase activities to genes important for haematopoietic differentiation, RAR signaling and epigenetic control is crucial to the transforming potential of PML-RAR/RXR.

overall_design: Examination of PML, RARa and RXR binding sites in leukemic cells before and after ATRA treatment, association with transcription via RNAPII occupancy and with chromatin modifications.

first: Henk

first: Joost

last: Martens

first: Arie

middle: B

last: Brinkman

first: Femke

last: Simmer

first: Kees-Jan

last: Francoijs

first: Angela

last: Nebbioso

first: Felicetto

last: Ferrara

first: Lucia

last: Altucci


title: PTB CLIP-seq

city: La Jolla

first: Xiang-Dong

last: Fu

address: 9500 Gilman Drive, Room 231

department: CMM

institute: UC San Diego

summary: Recent transcriptome analysis indicates that >90% of human genes undergoes alternative splicing, underscoring the contribution of differential RNA processing to diverse proteomes in higher eukaryotic cells. The polypyrimidine tract binding protein PTB is a well-characterized splicing repressor, but PTB knockdown causes both exon inclusion and skipping. Genome-wide mapping of PTB-RNA interactions and construction of a functional RNA map now revealed that dominant PTB binding near a competing constitutive splice site generally induces exon inclusion whereas prevalent binding close to an alternative site often causes exon skipping. This positional effect was further demonstrated by disrupting or creating a PTB binding site on minigene constructs and testing their responses to PTB knockdown or overexpression. These findings suggest a mechanism for PTB to modulate splice site competition to produce opposite functional consequences, which may be generally applicable to RNA binding splicing factors to positively or negatively regulate alternative splicing in mammalian cells.

overall_design:
Examination of PTB-RNA binding in Hela cells using CLIP-seq (Cross-Linking ImmunoPrecipitation coupled with high-throughput sequencing) method.

Peaks: The four alignment files (linked as supplementary files on Sample records) were combined together for peak finding, as we found that most of the monomeric and dimeric tags are similarly distributed in the genome with high pearson correlation coefficient. The method to detect the peaks above gene-specific randomized background was similar to (Yeo et al., 2009) and described in the paper (Xue et al., 2009).

first: Yuanchao

last: Xue

first: Yu

last: Zhou

first: Tongbin

last: Wu

first: Tuo

last: Zhu

first: Xiong

last: Ji

first: Young-Soo

last: Kwon

first: Chao

last: Zhang

first: Gene

last: Yeo

first: Douglas

last: Black

first: Hui

last: Sun

first: Yi


title: Genomic targets of the KRAB and scan domain-containing zinc finger protein 263 (ZNF263).

status: Public on Dec 03 2009

first: Flora

last: Vaccarino

summary:
Half of all human transcription factors use C2H2 zinc finger domains to specify site-specific DNA binding and yet very little is known about their role in gene regulation. Based on in vitro studies, a zinc finger code has been developed that predicts a binding motif for a particular zinc finger factor (ZNF). However, very few studies have performed genome-wide analyses of ZNF binding patterns and thus it is not clear if the binding code developed in vitro will be useful for identifying target genes of a particular ZNF. We performed genome-wide ChIP-seq for ZNF263, a C2H2 ZNF that contains 9 finger domains, a KRAB repression domain, and a SCAN domain and identified more than 5000 binding sites in K562 cells. Our results suggest that ZNF263 binds to a 24 nt site which differs from the motif predicted by the zinc finger code in several positions. Interestingly, many of the ZNF263 binding sites are located within the transcribed region of the target gene. Although ZNFs containing a KRAB domain are thought to function mainly as transcriptional repressors, many of the ZNF263 target genes are expressed at high levels. To address the biological role of ZNF263, we identified genes whose expression was altered by treatment of cells with ZNF263-specific siRNAs. Our results suggest that ZNF263 can have both positive and negative effects on transcriptional regulation of its target genes.

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: Examination of ZNF263 ChIP-seq in K562 cells.

first: Seth

last: Frietze

first: Peggy

last: Farnham


title: Genome-wide maps of Tbx3 binding sites in mouse ESCs

status: Public on Dec 04 2009

city: Singapore

first: Yuriy

last: Orlov

address: 60 Biopolis Street

department: Computational Systems Biology

institute: Genome Institute of Singapore

summary: Induced pluripotent stem (iPS) cells can be obtained through the introduction of defined factors into somatic cells. The combination of Oct4, Sox2 and Klf4 (OSK) constitutes the minimal requirement for generating iPS cells from mouse embryonic fibroblasts (MEFs). Through the genomic analyses of ESC genes that have roles in pluripotency and fusion-mediated somatic cell reprogramming, we identified Tbx3 as a transcription factor that significantly improves the quality of iPS cells. Induced-PS cells generated with OSK + Tbx3 (OSKT) are superior in both germ cell contribution to the gonads and germ-line transmission frequency. However, global gene expression profiling could not distinguish between OSK and OSKT iPS cells. Genome-wide ChIP-sequencing analysis of Tbx3 binding sites in ESCs suggests that Tbx3 regulates pluripotency-associated and reprogramming factors, in addition to sharing many common downstream regulatory targets with Oct4, Sox2, Nanog and Smad1.

overall_design: ChIP-seq of Tbx3 binding in mouse ESCs

first: Bing

last: Lim

first: Wai-Leong

last: Tam


title: Uncovering small RNA-mediated responses to phosphate-deficiency in Arabidopsis by deep sequencing

status: Public on Dec 01 2009

city: Taichung

first: Li-Ching

last: Hsieh

address: 145 Xingda Rd.

department: Graduate Institute of Genomics and Bioinformatics

country: Taiwan

institute: National Chung Hsing University

summary:
Deep sequencing of Arabidopsis thaliana small RNAs was conducted to reveal microRNAs (miRNAs) and other small RNAs that were differentially expressed in response to phosphate (Pi) deficiency. About 3.5 million sequence reads corresponding to 0.6-1.2 million unique sequence tags from each Pi-sufficient or -deficient root or shoot sample were mapped to the Arabidopsis genome. We showed that upon Pi deprivation, the expression of miR156, miR399, miR778 and miR827 was induced, whereas the expression of miR169, miR395 and miR398 was repressed. We found crosstalks coordinated by these miRNAs under different nutrient deficiencies. Moreover, we found a new miRNA family upregulated specifically by Pi deficiency. In addition to miRNAs, we identified one Pi starvation-induced DCL1-dependent small RNA derived from the long terminal repeat of a retrotransposon and a group of 19-nucleotide small RNAs corresponding to the 5' end of tRNA and expressed at a high level in Pi-starved roots. Interestingly, we observed an increased abundance of TAS4-derived trans-acting siRNAs (ta-siRNAs) in Pi-deficient shoots and uncovered an autoregulatory mechanism of PAP1/MYB75 via miR828 and TAS4-siR81(-) that regulates the biosynthesis of anthocyanin. This finding sheds light on the regulatory network between miRNA/ta-siRNA and its target gene. Of note, a substantial amount of miR399* accumulated under Pi deficiency. Like miR399, miR399* can move across the graft junction, implying a potential biological role for miR399*. This study represents a comprehensive expression profiling of Pi-responsive small RNAs and advances our understanding of the regulation of Pi homeostasis mediated by small RNAs.

Keywords: Transcriptome analysis

overall_design: Examination of 4 samples from root and shoot tissues of Arabidopsis in either phosphate-sufficient or phosphate-deficient condition

first: Tzyy-Jen

last: Chiou

first: Wen-Hsiung

last: Li

first: Shu-I

last: Lin

first: Arthur

last: Shih

first: June-Wei

last: Chen

first: Wei-Yi


title: Chromatin Profiling by Directly Sequencing Small Quantities of Immunoprecipitated DNA

status: Public on Nov 29 2009

first: Alon

last: Goren

institute: Broad Institute

summary: Chromatin structure and transcription factor localization can be assayed genome-wide by sequencing genomic DNA fractionated by protein occupancy or other properties. However, current technologies involve multiple steps that introduce bias and inefficiency. Here we apply a single-molecule approach to directly sequence chromatin immunoprecipitated DNA with minimal sample manipulation. This method is accurate, compatible with just 50 picograms of DNA and should thus facilitate charting chromatin maps from limited cell populations.

overall_design: Application of a single-molecule approach to directly sequence chromatin immunoprecipitated DNA of the CTCF DNA binding protein.

first: Bradley

middle: E

last: Bernstein


title: Global Analysis of Short RNAs Reveals Widespread Promoter-Proximal Stalling and Arrest of Pol II

status: Public on Dec 11 2009

city: Research Triangle Park

first: Sergei

last: Nechaev

state: NC

address: 111 Alexander Dr

department: Laboratory of Molecular Carcinogenesis

institute: NIEHS/NIH

summary: We developed a novel approach to isolate and characterize, at nucleotide-level resolution, the RNAs derived from RNA polymerase II (Pol II) in early elongation complexes. We find that high numbers of these short RNAs are not correlated with gene expression but instead are indicative of promoter-proximally stalled polymerase. High amounts of these short RNAs are generated from more than one third of all genes, indicating that Pol II  stalls in the promoter-proximal region on  global scale. We also find that the nucleotide composition of the initially transcribed sequence plays an important role in promoting transcriptional stalling and that early elongation complexes are highly susceptible to backtracking and arrest.

overall_design: Global analysis of RNAs produced by promoter-proximal Pol II.

first: David

last: Fargo

first: Gilberto

last: DosSantos

first: Liwen

last: Liu

first: Yuan

last: Gao

first: Karen

last: Adelman


status: Public on Nov 24 2009

city: Groningen

first: Eugene

last: Berezikov

address: Antonius Deusinglaan 1

department: European Research Institute for the Biology of Ageing

institute: University Medical Center Groningen

summary: High-throughput sequencing of Drosophila pseudoobscura and Drosophila simulans small RNAs. ~18-26nt RNAs were isolated from total RNA using PAGE, ligation to adapters requires 5' monophosphate and 3' OH.

sample_organism:
Drosophila pseudoobscura
Drosophila simulans

overall_design: Small RNAs were cloned from Drosophila pseudoobscura (heads and pooled 0-12 and 12-24 hour embryos) and Drosophila simulans (pooled 0-12 and 12-24 hour embryos). Sequencing was performed using the Illumina 1G platform.  Following removal of 3' linker sequences, the clipped sequences longer than 18 nt were kept.

first: E

first: N

first: A

middle: S

last: Flynt

last: Lai