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

city: Shenzhen

first: Hong

middle: zhi

last: Cao

state: Guangdong

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

department: Bioinformatics

institute: BGI-SHENZHEN

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

sample_organism:
Camponotus floridanus
Harpegnathos saltator

overall_design: Total RNA were isolated from virgin queens and queens by pulverizing the entire animal after removal of gut and poison glands in liquid N2 and then dissolving in TRIzol. PolyA+ RNA were prepared for deep sequencing.

first: Roberto

last: Bonasio

first: Qiye

last: Li

first: Guojie

last: Zhang

first: Danny

last: Reinberg


title: KAP1 regulates gene networks controlling T cell development and activation

status: Public on Aug 08 2012

city: Milan

first: Francesca

middle: R.

last: Santoni de Sio

address: via Olgettina 58

department: SR-TIGET

country: Italy

institute: San Raffaele Scientific Institute

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Drosophila melanogaster small RNA sequence: S2-DRSC cells (Rubin lab)

status: Public on Aug 09 2012

city: Toronto

first: DCC

last: modENCODE

state: Ontario

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

country: Canada

institute: Ontario Institute for Cancer Research

type: Non-coding RNA profiling by high throughput sequencing

summary:
modENCODE_submission_2725
This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA 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: EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male;  EXPERIMENTAL FACTORS: Cell Line S2-DRSC (Rubin); Replicate type: biological

first: Eric

last: Lai


title: Systematic RNA-seq analysis of the early events of CD4+ T cell activation

first: Andrew

middle: P

last: Hutchins

address: 1088 Xueyuan Rd

country: China

institute: Southern University of Science and Technology

type: Expression profiling by high throughput sequencing

summary: RNA-seq was used to look at the transcriptome changes and the early events of T cell receptor stimulation in CD4+ T cells

overall_design: CD4+ T cells were stimulated with immobilised anti-CD3/CD28 antibodies for 4 hours and RNA was extracted and subjected to RNA-seq analysis.

first: Diego

last: Miranda-Saavedra


title: Genome-wide analysis of global and caste-specific DNA methylation in two ant species: Camponotus floridanus and Harpegnathos saltator

type: Methylation profiling by high throughput sequencing

platform_organism:
Camponotus floridanus
Harpegnathos saltator


title: Single base resolution methylome of two ants: Camponotus floridanus and Harpegnathos saltator

summary: Deep BS-Seq of two Ants: Camponotus floridanus and Harpegnathos saltator.

overall_design: Up to 20 µg of total genomic DNA were isolated from embryos, larvae, males, virgin queens and queens for both species, as well as major and minor workers for C. floridanus, and workers and gamergates for H. saltator. DNA was fragmented by sonication with a Covaris S2 system (Covaris, MA) to a mean size of approximately 150 bp, followed by end-repair, 3'-end addition of dA, and adapter ligation. Methylated adapters were used according to the manufacturer's instructions (Illumina). The bisulfite conversion of sample DNA was carried out using a modified NH4SO4-based protocol and amplified by 9 cycles of PCR. Pair-end sequencing was carried out using Illumina Genome Analyzers.


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

city: HangZhou

first: Ding

last: He

state: ZheJiang

address: YuHangTang road

department: College of Life Science

institute: ZheJiang University

summary: We report the application of Solexa/Illumina’s RNA-seq sequencing approaches for transcriptome in a marine fish under different conditions (bacterial- and mock-challenged conditions). By obtaining over four billion bases of sequence from the cDNA, we generated 169,950 none-redundant consensus sequences, from which 44842 functional transcripts with complete or various length of encoding regions were identified. More than 52% of these transcripts could be enriched in approximately 219 known metabolic or signaling pathways, among of which 2673 transcripts were found to be associated with immune-relevant genes. Besides, about 8% of the transcripts seemed fish-specific genes that have never been described before. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations. Our study provided a global survey of the gene activities in host defense against bacterial infection in a non-model marine fish.

overall_design: Examination of different transcriptome in baterial- and mock challenged fish.

first: Jian-zhong

last: Shao

first: Li-xin

last: Xiang

first: Wei-ren

last: Dong

first: Yiwen


title: smRNA sequencing of queen and virgin queen of two ants: Camponotus floridanus and Harpegnathos saltator

summary: Deep sequencing of smRNA from queen and virgin queen of two Ants: Camponotus floridanus and Harpegnathos saltator

overall_design: Total RNA were isolated from virgin queens and queens by pulverizing the entire animal after removal of gut and poison glands in liquid N2 and then dissolving in TRIzol. Gel-purified 18-30 nts RNAs were used for sequencing.


title: Human-specific patterns of gene expression in the brain

status: Public on Sep 04 2012

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

country: USA

institute: UT Southwestern Medical Center

sample_organism:
Macaca mulatta
Pan troglodytes
Homo sapiens


title: Genome wide mapping of histone acetyltransferase MOF binding in murine ES cells (sequencing)

city: Ann Arbor

first: Yali

last: Dou

state: MI

address: Rm 5215A, MS I, 1301 Catherine Rd,

department: Department of Pathology, Department of Biological Chemistry

institute: University of Michigan

summary: We report the application of illumina sequencing technology for high-throughput profiling of histone acetyltransferase Mof in mouse embryonic stem cells. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse embryonic stem cells. We find that Mof widely binds to mouse genome and mark genes that are expressed, poised for expression, or stably repressed. Mof binds to both gene promoters and coding regions, exhibiting two modes of binding. This study provides a framework for understanding the function of Mof in regulating ESC core transcription network.

overall_design: Examination of Mof binding patterns in ES cells

first: Xiangzhi

first: Li

first: Ruichi

last: Pandey

first: Jung

last: Byun

first: Kevin

last: Gardner

first: Zhaohui

last: Qin


title: HSF1 drives a transcriptional program distinct from heat shock to support highly malignant human cancers [ChIP-Seq]

status: Public on Aug 07 2012

city: Cambridge

first: Marc

last: Mendillo

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: Heat-Shock Factor 1 (HSF1), master regulator of the heat-shock response, facilitates malignant transformation, cancer cell survival and proliferation in model systems. The common assumption is that these effects are mediated through regulation of heat-shock protein (HSP) expression. However, the transcriptional network that HSF1 coordinates directly in malignancy and its relationship to the heat-shock response have never been defined. By comparing cells with high and low malignant potential alongside their non-transformed counterparts, we identify an HSF1-regulated transcriptional program specific to highly malignant cells and distinct from heat shock. Cancer-specific genes in this program support oncogenic processes: cell-cycle regulation, signaling, metabolism, adhesion and translation. HSP genes are integral to this program, however, even these genes are uniquely regulated in malignancy. This HSF1 cancer program is active in breast, colon and lung tumors isolated directly from human patients and is strongly associated with metastasis and death.  Thus, HSF1 rewires the transcriptome in tumorigenesis, with prognostic and therapeutic implications.

overall_design: ChIP-seq was used to characterize HSF1 binding

middle: L

first: Sandro

last: Santagata

first: Martina

last: Koeva

first: George

middle: W

last: Bell

first: Rong

last: Hu

first: Rulla

middle: M

last: Tamimi

first: Ernest

last: Fraenkel

first: Tan

middle: A

last: Ince

first: Luke

last: Whitesell

first: Susan

last: Lindquist


title: DNA methyltransferases are required to induce heterochromatic re-replication in Arabidopsis.

first: Hume

last: Stroud

address: 5323 Harry Hines Blvd

institute: UT Southwestern

type: Genome variation profiling by high throughput sequencing

summary: The relationship between epigenetic marks on chromatin and the regulation of DNA replication is poorly understood. Mutation of the H3K27 methyltransferase genes, ARABIDOPSIS TRITHORAX-RELATED PROTEIN5 (ATXR5) and ATXR6, result in re-replication (repeated origin firing within the same cell cycle). Here we show that mutations that reduce DNA methylation act to suppress the re-replication phenotype of atxr5 atxr6 mutants. This suggests that DNA methylation, a mark enriched at the same heterochromatic regions that re-replicate in atxr5/6 mutants, is required for aberrant re-replication. In contrast, RNA sequencing analyses suggest that ATXR5/6 and DNA methylation cooperatively transcriptionally silence transposable elements (TEs). Hence our results suggest a complex relationship between ATXR5/6 and DNA methylation in the regulation of DNA replication and transcription of TEs.

overall_design:
DNA-seq: One gram of mature rosette leaves were collected from 3-4-week-old plants, chopped in 0.5 ml of filtered Galbraith buffer, and stained with propidium iodide. A BD FACS Aria II in the UCLA Jonsson Comprehensive Cancer Center (JCCC) Flow Cytometry Core Facility was used to sort the nuclei.  For sequencing, 7,000-9,000 8C nuclei of each sample were collected, and purified DNA with Picopure purification kit (Arcturus) following manufacturer instructions.

RNA-seq: RNA-seq experiments were performed in two biological replicates for each genotype. 0.1g of tissue was ground in Trizol.  Total RNA were treated with DNaseI (Roche), and cleaned up with phenol-chlorophorm and precipitated with ethanol. Libraries were generated and sequenced following manufacturer instructions (Illumina).

BS-seq: 0.5-1g of mature rosette leaves were collected, and genomic DNA was extracted using Plant DNeasey mini purification kit (Qiagen). Libraries were generated as previously described (Feng et al., Methods Mol Biol. 2011;733:223-38.).


title: ChIP-seq study of BEAF binding in four Drosophila spcies

status: Public on Aug 03 2012

city: Nanjing

first: Jingping

last: Yang

state: Jiangsu

address: 22 Hankou Road

department: Medical School

institute: Nanjing University

summary: Insulators are considered as chromosome organizers. BEAF, one of the insulator proteins, is highly conserved in Drosophila speies but also limited to Drosophila spcies. BEAF associates with TSS of active genes. Comparative study of BEAF binding landscapes in four Drosophila species reveals BEAF association with gene pairs, and the results suggest the role of gain or loss of BEAF binding during the speciation of Drosophila species.

sample_organism:
Drosophila melanogaster
Drosophila pseudoobscura
Drosophila simulans
Drosophila virilis

overall_design: DNA sample from ChIP for BEAF and input are collected for each of four Drosophila species

first: Victor

last: Corces


title: RNA-Seq of cKIT+ sorted cells from 16-16.5 week old fetal testes and ovaries and RNA-Seq of TRA-1-60+ H1 hESCs

city: Los Angeles

first: Sofia

last: Gkountela

state: California

address: 621 Charles E Young Dr S

department: MCDB

institute: UCLA

summary: Generation of research quality, clinically relevant cell types in vitro from human pluripotent stem cells (hPSCs) requires detailed understanding of the equivalent cell types in humans. Here we analyzed 130 human fetal samples at 6-20 weeks of development and identified the stages in which human cKIT+ primordial germ cells (PGCs), the precursors of gametes, undergo whole genome epigenetic reprogramming and ultimately initiation of imprint erasure with loss of both 5mC and 5-hydroxy-mC at differentially methylated regions. Using five alternate in vitro differentiation strategies combined with a single-cell microfluidic analysis, high throughput RNA sequencing and a bona fide human cKIT+ PGC signature, we show that hPSC differentiation generates a rare cKIT+ PGC subtype found in both the human fetal gonad and mouse embryo. Taken together, our study creates a resource of human germ line ontogeny that is absolutely essential for future studies aimed at interpreting in vitro differentiation of the human germ line.

overall_design: cKIT+ cells analyzed from 2 biological samples for testes and 2 samples for ovaries at 16 and 16.5 weeks. 3 biological replicates of TRA-1-60+ cells sorted from H1 hESCs

first: Ziwei

last: Li

first: John

middle: J

last: Vincent

first: Kelvin

middle: X

last: Zhang

first: Angela

last: Chen

first: Matteo

last: Pellegrini

first: Amander

middle: T

last: Clark


title: A small RNA response to DNA ends in Drosophila

city: Munich

first: Klaus

last: Förstemann

address: Feodor-Lynen 25

department: Gene Center

country: Germany

institute: Ludwig-Maximilians University

summary: Small RNAs have been implicated in numerous cellular processes, including effects on chromatin structure and the repression of transposons. We describe the generation of a small RNA response at DNA ends in Drosophila that is analogous to the recently reported DSB-induced RNAs (diRNAs) or Dicer and Drosha dependent small RNAs (ddRNAs) in Arabidopsis and vertebrates. Active transcription in the vicinity of the break amplifies this small RNA response, demonstrating that the normal mRNA contributes to the endo-siRNA precursor. The double-stranded RNA precursor forms with an antisense transcript that initiates at the DNA break. Breaks are thus sites of transcription initiation, a novel aspect of the cellular DSB response. This response is specific to a double-strand break since nicked DNA structures do not trigger small RNA production. The small RNAs are generated independently of the exact end structure (blunt, 3'- or 5'-overhang), can repress homologous sequences in trans and may therefore - in addition to putative roles in repair - exert a quality control function by clearing potentially truncated messages from genes in the vicinity of the break.

overall_design: Drosophila melanogaster S2 cells were cultured and transfected with reporter gene plasmids that were either circular or modified by restriction digest prior to transfection. Following transfection, total RNA was isolated from the cells and gel-purified for size selection (~18-30 nt). Digested plasmid samples were compared to those of circular plasmids and a nontransfected control.

last: Forstemann


title: Drosophila melanogaster Canton-S small RNA sequence: Adult Male Head

status: Public on Aug 10 2012

first: DCC

last: modENCODE

summary:
modENCODE_submission_747
This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA 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: EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Strain: Canton S; Tissue: Male body; Developmental Stage: Adult male; Genotype: wild type; Sex: Male; EXPERIMENTAL FACTORS: Strain Canton S; Tissue Male head; Developmental Stage Adult male; Replicate type: biological;

first: Eric

last: Lai


title: HSF1 drives a transcriptional program distinct from heat shock to support highly malignant human cancers

first: Marc

last: Mendillo


title: Characterization of microRNAs expression during maize seed development

city: Beijing

first: Mingming

last: Kang

address: No. 2 Yuanmingyuan West Rd,

institute: China Agricultural University

summary: In this study, two small RNA libraries were sequenced, and a total reads of 9,705,761 and 9,005,563 were generated from developing seeds and growing leaves, respectively. Further analysis identified 125 known miRNAs in seeds and 127 known miRNAs in leaves. 54 novel miRNAs were identified and they were not reported in other plants.

overall_design: Identification of known and novel miRNAs essential to maize seed development

first: Qian

last: Zhao

first: Dengyun

last: Zhu

first: Jingjuan

last: Yu


title: IBM1, a JmjC domain histone demethylase, is involved in the regulation of RNA-directed DNA methylation through epigenetic control of RDR2 and DCL3 expression in Arabidopsis.

first: Di

last: Fan

state: Beijing

address: 7# Science Park Road Zhongguancun Life Science Park

institute: National Institute of Biological Sciences

summary: The small RNA mediated DNA methylation (RdDM) is highly elaborated in Arabidopsis as an important epigenetic pathway controls expression of genes and multiple developmental processes. RDR2 and DCL3 are necessary factors to the 24-nt siRNA biogenesis and the RdDM pathway. Here, we find that IBM1 (increase in BONSAI methylation 1), a conserved JmjC family histone demethylase, could directly associated with the chromatin of RDR2 and DCL3. The IBM1 mutation induces hypermethylation on both H3K9 and DNA non-CG sites in these loci, and further represses their expression. The reduction of RDR2 and DCL3 may affect siRNA biogenesis in a locus-specific manner and disrupt the RdDM directed repression. It suggests an indirect way to regulate targets by IBM1 through control of siRNA biogenesis, and demonstrate the relationship between histone methylation and small RNAs.

overall_design: Genome-wide integrated mapping of mRNA transcripts and small RNAs, using whole plant of 10-days seedlings of the Columbia-0 wildtype and ibm1-3 mutant Arabidopsis thaliana.

first: Xuncheng

last: Wang

first: Jianguang

first: Ligeng

last: Ma


title: Tryptamine Serves As a Proligand of the AhR Transcriptional Pathway, and the Activation Is Dependent of Monoamine Oxidases

status: Public on Aug 02 2012

first: Bernward

last: Klocke

address: Bayerstr. 85a

institute: Genomatix Software GmbH

summary: In this study we show that physiological concentrations of tryptamine (TA) lead to induction of cytochrome P4501A1 transcription through an AhR-dependent mechanism. In addition, we show that activation of the AhR by TA requires a functional monoamino oxidase system, suggesting that TA acts as an AhR proligand possibly by converting to a high-affinity AhR ligand.

overall_design: RNA seq was performed from Hepa cells treated with FICZ or TA by SciLifelabs.

first: Linda

middle: V

last: Bergander

first: Wen

last: Cai

first: Martin

last: Seifert

first: Ingemar

last: Pongratz


title: Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting

city: Kiel

first: Mario

last: Brosch

address: Schittenhelmstr. 12

department: 1. Medical Department

institute: University Hospital Kiel

summary: So far, the annotation of translation initiation sites (TISs) has been based mostly upon bioinformatics rather than experimental evidence. We adapted ribosomal footprinting to puromycin-treated cells to generate a transcriptome-wide map of TISs in a human monocytic cell line. A neural network was trained on the ribosomal footprints at previously annotated AUG translation initiation codons (TICs), and used for the ab initio prediction of TISs in 5062 transcripts with sufficient sequence coverage. Functional interpretation suggested 2994 novel upstream open reading frames (uORFs) in the 5´ UTR (924 AUG, 2070 near-cognate codons), 1406 uORFs overlapping with the coding sequence (116 AUG, 1290 near-cognate) and 546 N-terminal protein extensions (6 AUG, 540 near-cognate). The TIS detection method was validated on the basis of previously published alternative TISs and uORFs. On average, TICs in newly annotated TISs were significantly more conserved among primates than control codons, both for AUGs (p<10-10) and near-cognate codons (p=3.8×10-3). The derived transcriptome-wide map of novel candidate TISs will help to explain how human proteome diversity is influenced by alternative translation initiation and regulation.

overall_design: Examination of translational initiation in human cell lines using ribosomal footprinting

first: Claudia

last: Fritsch

first: Alexander

last: Herrmann

first: Michael

last: Nothnagel

first: Karol

last: Szafranski

first: Klaus

last: Huse

first: Frank

last: Schumann

first: Stefan

last: Schreiber

first: Matthias

last: Platzer

last: Krawczak

first: Jochen

last: Hampe


title: MicroRNA expression profiling after short-term exposure to TCDD in zebrafish embryos

city: Woods Hole

first: Neelakanteswar

last: Aluru

address: 45 Water Street

department: Biology

institute: Woods Hole Oceanographic Institution

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

platform_organism:
Danio rerio
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human betaherpesvirus 5
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Human gammaherpesvirus 8
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: Refer to individual Series


title: MicroRNA expression profiling after short-term exposure to TCDD in zebrafish embryos [miRNA-Seq data]

summary: Although many drugs and environmental chemicals are teratogenic, the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs (miRNAs),  single-stranded RNA molecules of ~22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation, are important regulators of a variety of cellular processes including embryonic development and cellular differentiation.  We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well-known teratogen, we exposed zebrafish embryos to DMSO (0.1%) or TCDD (5 nM) for 1 hr at 30 hours post fertilization (hpf) and measured microRNA expression using several methods at 36 and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf (62-fold) and 60 hpf (135-fold) as determined by qPCR, verifying the  effectiveness of the exposure.  microRNA expression profiles were determined using microarrays (Agilent and Exiqon), next-generation sequencing (SOLiD) and real time RT-PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR-451, 23a, 23b, 24 and 27e at 60 hpf.  Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos.  However, miR-27e was the only miRNA to be identified as differentially expressed by all three methods (both microarrays, SOLiD sequencing, and qPCR).  These results suggest that TCDD exposure causes modest changes in expression of microRNAs, including some (miR-451, 23a, 23b, 24 and 27e) that are critical for hematopoiesis and cardiovascular development.

overall_design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing

first: Matthew

last: Jenny

first: Mark

middle: E

last: Hahn


title: Regulatory element copy number differences shape primate expression profiles.

city: Tucson

first: Darren

middle: A.

last: Cusanovich

state: AZ

address: 1230 N Cherry Avenue, BSRL 421

department: Cellular and Molecular Medicine

institute: University of Arizona

summary: Gene expression differences are shaped by selective pressures and contribute to phenotypic differences between species. We identified 964 copy number differences (CNDs) of conserved sequences across 3 primate species and examined their potential effects on gene expression profiles. Samples with copy number different genes had significantly different expression than samples with neutral copy number. Genes encoding regulatory molecules differed in copy number and were associated with significant expression differences. Additionally, we identified 127 CNDs which were processed pseudogenes and some of which were expressed. Furthermore, there were copy number different regulatory regions such as ultraconserved elements and long intergenic noncoding RNAs with the potential to affect expression. We postulate that CNDs of these conserved sequences fine-tune developmental pathways by altering the levels of RNA.

sample_organism:
Macaca mulatta
Pan troglodytes

platform_organism:
Macaca mulatta
Pan troglodytes

overall_design: Gene expression patterns were compared between human, chimpanzee and rhesus macaque lymphoblastoid cell lines using RNA-Seq. Samples from 6 individuals of each species were used. The 6 human samples were previously published as a part of GEO record GSE19480 (samples GSM485426, GSM485428, GSM485468, GSM485410, GSM485413 and GSM485414). The 6 chimpanzee and 6 rhesus macaquesamples are included in the current record (GSE38572).

first: Rebecca

middle: C

last: Iskow

first: Omer

last: Gokcumen

first: Alexej

last: Abyzov

first: Joanna

last: Malukiewicz

first: Qihui

last: Zhu

first: Ann

last: Sukumar

first: Athma

last: Pai

first: Ryan

last: Mills

first: Lukas

last: Habegger

first: Meagan

last: Rubel

first: George

last: Perry

last: Gerstein

first: Anne

last: Stone

first: Yoav

last: Gilad

first: Charles

last: Lee


title: Small RNAs in tgh-1 mutant

city: Lincoln

first: Bin

last: Yu

state: NE

address: 1901 Vine Street

department: Biological Sciences

institute: University of Nebraska - Lincoln

summary: miRNAs are regulators of gene expression in plants and animals. Their biogenesis is precisely controlled to secure normal development of organisms.  Here we report that TOUGH (TGH) is a novel component of DCL1-HYL1-SE complex that processes of primary transcripts of miRNAs (pri-miRNAs) into miRNAs in Arabidopsis.  Lack of TGH impairs multiple DCL activities in vitro and reduces the accumulation of miRNAs and siRNAs in vivo. TGH is an RNA binding protein, binds with pri-miRNAs in vivo and contributes to pri-miRNA-HYL1interaction. These results indicate that TGH might regulate abundance of miRNAs through promoting the DCL1 cleavage efficiency and/or recruitment of pri-miRNAs. Because TGH is a conserved protein in plants and animals, our study shall have implications on miRNA pathway in other organisms

overall_design: tgh-1 mutant vs. wild type

first: Yu

last: Bin

first: Ren

last: Guodong

first: Zhang

last: Chi


title: Mouse ooplasm confers context-specific reprogramming capacity

city: San Francisco

first: Michelle

last: Chan

state: CA

institute: UCSF

summary: Enucleated oocytes have the remarkable ability to reprogram somatic nuclei back to totipotency. Here we investigate genome-scale DNA methylation patterns after nuclear transfer and identify specific targets for DNA demethylation as well as NT specific limitations. We find that the ooplasm can confer similar demethylation patterns in both processes except at some repetitive element classes and that germ-line associated promoters are specifically targeted in NT.

overall_design: Comparison of DNA methylation patterns in murine fertilization and somatic cell nuclear transfer

first: Zachary

middle: D

last: Smith

first: Dieter

last: Egli

first: Aviv

last: Regev

first: Alexander

last: Meissner


title: Mixture models and wavelet transforms reveal high confidence RNA-protein interaction sites in MOV10 PAR-CLIP data

city: Basel

first: Cem

last: Sievers

address: Mattenstrasse

country: Switzerland

institute: ETH Zurich

summary: The Photo-Activatable Ribonucleoside-enhanced CrossLinking and ImmunoPrecipitation (PAR-CLIP) method was recently developed for global identification of RNAs interacting with proteins. The strength of this versatile method results from induction of specific T to C transitions at sites of interaction. However, current analytical tools do not distinguish between non-experimentally and experimentally induced transitions. Furthermore, geometric properties at potential binding sites are not taken into account. To surmount these shortcomings, we developed a two-step algorithm consisting of a non-parametric two-component mixture model and a wavelet-based peak calling procedure. Our algorithm can reduce the number of false positives up to 24% thereby identifying high confidence interaction sites. We successfully employed this approach in conjunction with a modified PAR-CLIP protocol to study the functional role of nuclear MOV10, a putative RNA helicase interacting with Argonaute2 and Polycomb. Our method, available as the R package wavClusteR, is generally applicable to any substitution-based inference problem in genomics.

overall_design: The data comprises one MOV10 PAR-CLIP data file and one nuclear RNA-seq file

first: Renato

last: Paro


title: Cell type-specific gene expression profiling of Drosophila neurons [RNA-Seq]

city: Ashburn

first: Fred

last: Davis

state: VA

address: 19700 Helix Dr

institute: HHMI Janelia Farm Research Campus

summary: Gene expression profiling of nuclei isolated from genetically defined neuronal subpopulations of the adult Drosophila brain.

overall_design: Gene expression profiles were generated from nuclei isolated from all neurons (R57C10-GAL4), Kenyon cells (OK107-GAL4), and octopaminergic (Tdc2-GAL4) neurons in the adult Drosophila head using a method similar to INTACT (Deal and Henikoff, 2010; Steinner et al., 2012). Sequencing was performed with an Illumina HiSeq 2000.

first: Gilbert

last: Henry

first: Serge

last: Picard

first: Sean

middle: R

last: Eddy


title: The DDR complex facilitates the genome-wide association of RNA Polymerase V to promoters and evolutionarily young transposons

status: Public on Aug 05 2012

city: Seattle

first: Christopher

middle: Joel

last: Hale

state: WA

address: 1959 NE Pacific St., HSC H-458

department: Pathology

institute: University of Washington

summary: The plant-specific DNA-dependent RNA polymerase V (Pol V) evolved from Pol II to function in an RNA-directed DNA methylation pathway. Here, we have identified targets of Pol V in Arabidopsis thaliana on a genome-wide scale using ChIP-seq of NRPE1, the largest catalytic subunit of Pol V. We found that Pol V is enriched at promoters and evolutionarily recent transposons. This localization pattern is highly correlated with Pol V-dependent DNA methylation and small RNA accumulation. We also show that genome-wide association of Pol V with chromatin is dependent on all members of a putative chromatin-remodeling complex termed DDR. Our study presents the first genome-wide view of Pol V occupancy and sheds light on the mechanistic basis of Pol V localization. Furthermore, these findings suggest a role for Pol V and RNA-directed DNA methylation in genome surveillance and in responding to genome evolution.

overall_design: For wild type plants (ecotype Columbia) and nrpe1 mutants whole-genome small RNA (sRNA-seq) and bisulfite sequencing (BS-seq) was performed. In addition whole genome chromatin immunoprecipitation (ChIP-seq) was performed on wild type (ecotype Columbia) plants as a negative control with experimentals consiting of wild type plants carrying a C-terminally epitope tagged (2XFLAG) NRPE1, as well as the NRPE1-FLAG construct in drd1, dms3, and rdm1 mutant backgrounds.


title: Identification of soybean seed developmental stage specific and tissue specific miRNA targets by degradome sequencing .

city: Urbana

first: Lila

middle: O.

last: Vodkin

state: IL

address: 1201 W. Gregory Dr.

department: Crop Sciences

institute: University of Illinois

summary: Five degradome libraries were constructed from three different seed developmental stages. Separate degradome libraries were constructed for seed coat and cotyledons to identify the tissue specific miRNAs and their potential targets. Sequencing and analysis of degradome libraries gives identification of 183 different targets for 80 known soybean miRNAs. We found 30 cotyledon specific, 18 seed coat specific and 32 miRNAs found in both tissues irrespective of the developmental stages. One interesting observation is that we found more miRNA targets in late seed developmental stages than earlier stages.  Additionally, we have validated four different auxin response factor genes as targets for gma-miR160 via RNA ligase mediated 5′ rapid amplification of cDNA ends (RLM-5′RACE). GO analysis indicated the enrichment of miRNA target genes in seed development.

overall_design: Construction of degradome libraries using cotyledons and seed coats from 3 different developmental stages

middle: O

first: Md

last: Shamimuzzaman


title: AGO4 Regulates Entry into Meiosis and Influences Silencing of Sex Chromosomes in the Male Mouse Germline

status: Public on Aug 01 2012

city: Ithaca

first: Stephanie

middle: Renee

last: Hilz

address: Biotech 445, Cornell University

institute: Cornell University

summary:
The four mammalian Argonaute family members are thought to share redundant functions in the microRNA pathway, yet only AGO2 possesses the catalytic "slicer" function required for RNA
interference. Whether AGO1, AGO3, or AGO4 possess specialized functions remains unclear. Here, we Series_summary = show that AGO4 localizes to spermatocyte nuclei during meiotic prophase I, specifically at sites of asynapsis and in the transcriptionally silenced XY sub-domain, the sex body. We generated Ago4 knockout mice and show that Ago4-/- spermatogonia initiate meiosis early, resulting from premature
induction of retinoic acid-response genes. During prophase I, the sex body assembles incorrectly in Ago4-/- mice, leading to disrupted meiotic sex chromosome inactivation (MSCI). This is associated
with a dramatic loss of microRNAs, >20% of which arise from the X chromosome. Loss of AGO4 results in increased AGO3 in spermatocytes, indicating some degree of redundancy. Thus, AGO4 regulates
meiotic entry and MSCI in mammalian germ cells, implicating small RNA pathways in these processes.

overall_design:
mRNA transcripts were isolated and prepared using pachytene spermatocytes, pre-meiotic testes and other tissues from Ago4+/+ and Ago4-/- littermates and sequenced using Illumina HiSeq2000.
small RNA transcripts were isolated and prepared using pachytene spermatocytes from adult Ago4+/+ and Ago4-/- littermates and sequenced using Illumina GAII.

first: Modzelewski

last: Modzelewski

first: Hilz

last: Stephanie

first: Grimson

last: Andrew

first: Cohen

last: Paula


title: A mutation in PP2C Phosphatase Gene in a Staphylococcus aureus USA300 Clinical Isolate with Reduced Susceptibility to Vancomycin and Daptomycin

city: Atlanta

first: Tim

last: Read

address: 615 Michael Street, Suite 301

institute: Emory University

summary: Investigation of baseline transcription activity of two different clinical isolates of Staphylococcus aureus with two different susceptibility levels to the antibiotics Vancomycin and Daptomycin.

overall_design: Two different strains of Staphylococcus aureus, one that is fully Vancomycin and Daptomycin Sensitive and one with decreased Vancomycin and Daptomycin Sensitivity - grown to mid-log phase in rich broth.

first: Karla

last: Passalacqua

first: Timothy

first: Sarah

last: Satola

first: Emily

middle: K

last: Crispell


title: Identification of miRNA signatures during the differentiation of hESCs into retinal pigment epithelial cells

first: Kevin

last: Huang

address: Gonda BLDG Rm. 6554, P.O.Box 957088

department: Human Genetics

summary: Retinal pigment epithelium (RPE) cells can be obtained through in vitro differentiation of both embryonic stem cell (ESC) and induced pluripotent stem cells (iPSC) for cell replacement therapy. We have previously identified 87 signature genes relevant to RPE cell differentiation and function through transcriptome analysis of both human ESC- and iPSC-derived RPE as well as normal fetal RPE. Here, we profiled miRNA expression through small RNA-seq in human ESCs and their RPE derivatives. Much like conclusions drawn from our previous transcriptome analysis, we found that the overall miRNA landscape in RPE is distinct from ESCs and other differentiated somatic tissues. We also profiled miRNA expression during intermediate stages of RPE differentiation and identified unique subsets of miRNAs that are gradually up- or downregulated, suggesting dynamic regulation of these miRNAs is associated with the RPE differentiation process. Indeed, the down-regulation of a subset of miRNAs during RPE differentiation is associated with up-regulation of RPE-specific genes, such as RPE65, which is exclusively expressed in RPE. We conclude that miRNA signatures can be used to classify different degrees of in vitro differentiation of RPE from human pluripotent stem cells. We suggest that RPE-specific miRNAs likely contribute to the functional maturation of RPE in vitro, similar to the regulation of RPE-specific mRNA expression.

overall_design: Study miRNA in ESC-derived RPE

first: Guoping

last: Fan


title: The X-linked H3K27me3 demethylase Utx is required for embryonic development in a sex specific manner

first: Albert

middle: W

last: Cheng

address: Room 453, 9 Cambridge Center

institute: Whitehead Institute

first: Grant

last: Welstead

first: Rudolf

last: Jaenisch


title: Cell type-specific chromatin profiling of Drosophila neurons [ChIP-Seq]

first: Fred

middle: P

last: Davis

summary: Chromatin profiling of nuclei isolated from genetically defined neuronal subpopulations of the adult Drosophila brain.

overall_design: Cell type-specific histone modification maps were generated from nuclei isolated from all neurons (R57C10-GAL4), Kenyon cells (OK107-GAL4), and octopaminergic (Tdc2-GAL4) neurons using a method similar to INTACT (Deal and Henikoff, 2010; Steinner et al., 2012). Three histone modifications were profiled: H3K4me3, H3K27ac, and H3K27me3. Sequencing was performed with an Illumina HiSeq 2000.

first: Gilbert

middle: L

last: Henry

first: Serge

last: Picard

first: Sean

last: Eddy


title: Cell type-specific gene expression and chromatin profiling of Drosophila neurons


title: The polyA+ transcriptomes of mouse embryonic stem cells and their derived neural precursors from strand-specific RNA-Seq

first: Courtney

last: Onodera

address: 1450 Third St, HD374

institute: University of California, San Francisco

summary: We have examined the nuclear (nuc) and cytoplasmic (cyt) polyA+ transcriptomes of undifferentiated mouse embryonic stem cells (un) and cells differentiated to neural precursors (d5) using strand-specific RNA-Seq. The 46C mouse embryonic stem cell line was used for this study.

overall_design: Two cell types were examined: undifferentiated mouse embryonic stem cells (un) and cells differentiated to neural precursors (d5). For each cell type, cells were fractionated to nuclear and cytoplasmic components. RNAs were extracted from each component and were fragmented enzymatically for library construction. For each cell type and component, strand-specific RNA-Seq libraries were generated using at least two different fragmentation protocols.

middle: S

first: Jason

middle: G

last: Underwood

first: Sol

last: Katzman

first: Frank

last: Jacobs

first: David

last: Greenberg

first: Sofie

last: Salama

last: Haussler


title: Genome-wide maps of nucleosome occupancy in human lymphoblastoid cell lines

city: La Jolla

first: Graham

last: McVicker

address: 10010 N Torrey Pines Rd

institute: Salk Institute

summary: Nucleosomes are important for gene regulation because their arrangement on the genome can control which proteins bind to DNA. Currently, few human nucleosomes are thought to be consistently positioned across cells; however, this has been difficult to assess due to the limited resolution of existing data. We performed paired-end sequencing of micrococcal nuclease-digested chromatin (MNase-seq) from seven lymphoblastoid cell lines and mapped over 3.6 billion MNase-seq fragments to the human genome to create the highest-resolution map of nucleosome occupancy to date in a human cell type. In contrast to previous results, we find that most nucleosomes have more consistent positioning than expected by chance and a substantial fraction (8.7%) of nucleosomes have moderate to strong positioning. In aggregate, nucleosome sequences have 10 bp periodic patterns in dinucleotide frequency and DNase I sensitivity; and, across cells, nucleosomes frequently have translational offsets that are multiples of 10 bp. We estimate that almost half of the genome contains regularly spaced arrays of nucleosomes, which are enriched in active chromatin domains. Single nucleotide polymorphisms that reduce DNase I sensitivity can disrupt the phasing of nucleosome arrays, which indicates that they often result from positioning against a barrier formed by other proteins. However, nucleosome arrays can also be created by DNA sequence alone. The most striking example is an array of over 400  nucleosomes on chromosome 12 that is created by tandem repetition of sequences with strong positioning properties. In summary, a large fraction of nucleosomes are consistently positioned-in some regions because they adopt favored sequence positions, and in other regions because they are forced into specific arrangements by chromatin remodeling or DNA binding proteins.

overall_design: MNase-seq of 7 human lymphoblastoid cell lines from the HapMap project

first: Daniel

middle: J

last: Gaffney

first: Athma

middle: A

last: Pai

first: Yvonne

middle: N

last: Fondufe-Mittendorf

first: Noah

last: Lewellen

first: Katelyn

last: Michelini

first: Yoav

last: Gilad

first: Jonathan

last: Pritchard


title: Proteo-Genomic Characterization and Mapping of Nucleosomes Decoded by Brd and HP1 Proteins

status: Public on Jul 31 2012

city: Cincinnati

first: Iouri

last: Chepelev

state: OH

address: 3200 Vine St

institute: US Department of Veterans Affairs Medical Center


title: Proteo-Genomic Characterization and Mapping of Nucleosomes Decoded by Brd and HP1 Proteins (Chip-Seq data)

summary:
Background: Histone post-translational modifications (PTMs) constitute a branch of epigenetic mechanisms that can control the expression of eukaryotic genes in a heritable manner. Recent studies have identified several PTM-binding proteins containing diverse specialized domains whose recognition of specific PTM sites leads to gene activation or repression. Here, we present a high-throughput proteogenomic platform designed to characterize the nucleosomal make-up of chromatin enriched with a set of histone PTM-binding proteins known as histone PTM readers. We support our findings with gene expression data correlating to PTM distribution.

Results: We isolated human mononucleosomes bound by the bromodomain-containing proteins Brd2, Brd3 and Brd4, and by the chromodomain-containing heterochromatin proteins HP1alpha and HP1beta. Histone PTMs were quantified by mass spectrometry (ChIP-qMS), and their associated DNAs were mapped using deep sequencing. Our results reveal that Brd- and HP1-bound nucleosomes are enriched in histone PTMs consistent with actively transcribed euchromatin and silent heterochromatin, respectively. Data collected using RNA-Seq (GSM301568) show that Brd-bound sites correlate with highly expressed genes. In particular, Brd3 and Brd4 are most enriched on nucleosomes located within HOX gene clusters, whose expression is reduced upon Brd4 depletion by shRNA.

Conclusions: Proteogenomic mapping of histone PTM readers, alongside the characterization of their local chromatin environments and transcriptional information, should prove useful for determining how histone PTMs are bound by these readers and how they contribute to distinct transcriptional states.

overall_design: Examination of Brd and HP1 proteins-binding sites in HEK293 cells.

first: Gary

last: LeRoy

first: Peter

last: DiMaggio

first: Mario

last: Blanco

first: Barry

middle: M

last: Zee

first: Keji

last: Zhao

first: Benjamin

last: Garcia


title: H4K20me1 contributes to downregulation of X-linked genes for Caenorhabditis elegans dosage compensation

city: Cambridge

first: Przemyslaw

middle: Aleksander

last: Stempor

state: United Kingdom

address: Tennis Court Road

department: The Gurdon Institute

country: United Kingdom

institute: University of Cambridge

summary: We compared the pattern of H4K20me1 at the L3 stage in wild-type and set-4 mutants by ChIP-seq. In wild-type, H4K20me1 levels on the X chromosome are higher than on autosomes. In set-4 mutants, this difference is lost.

overall_design: ChIP-seq of H4K20me1 at the L3 stage in wild-type and set-4 mutant L3 larvae.

first: Julie

last: Ahringer


title: Genome-wide analysis of histone methylation reveals chromatin state-based regulation of host cellular gene expression induced by hepatitis B viruses (DGE dataset)

city: Chongqing

first: Ni

last: Bing

address: PLA, Third Military Medical University

department: Institute of Immunology

institute: PLA, Third Military Medical University

summary: Hepatitis B virus (HBV) is a hepatotropic virus that can regulate many host cellular gene expressions participating in the HBV life cycle, liver inflammation and hepatocellular injury. However, the underlying mechanism of differential gene expression is not understood. We report here a genome-wide analysis of histone methylation on two histone H3 lysine residues (H3K4me3 and H3K27me3) and gene expression profiles in HepG2 and HepG2.2.15 cells. We found that specific correlation exists between gene expression and the amounts of H3K4me3 (positive correlation) and H3K27me3 (negative correlation) across the gene body. These correlations displayed three distinct modes (repressive, active and poised), reflecting different functions of these genes in the HBV life cycle, liver inflammation and hepatocellular injury. Furthermore, a permissive chromatin state of each gene was established by a combination of different histone modifications. Our findings reveal a complex regulation by histone methylation in differential gene expression and suggest that histone methylation may be responsible for the HBV life cycle, liver inflammation and hepatocellular injury induced by HBV.

overall_design: A large-scale analysis of gene expression of 2 different cell types (HepG2, HepG2.2.15) using a digital gene expression (DGE) tag profiling approach.

first: Yi

last: Tian

first: Bing

last: Ni

first: Yuzhang

last: Wu


title: Genome-wide analysis of histone methylation reveals chromatin state-based regulation of host cellular gene expression induced by hepatitis B viruses (ChIP-Seq dataset)

overall_design: Examination of 2 different histone modifications (H3K4me3, H3K27me3) in 2 cell types (HepG2, HepG2.2.15).


title: The epigenetic cell-cycle regulator HCF-1 is recruited to active CpG island-containing promoters together with the ZNF143, THAP11(Ronin), YY-1 and GABP transcription factors.

city: Lausanne

first: Nicolo

last: Riggi

state: VD

address: Bugnon 25

department: Département de Pathologie Expérimentale

institute: CHUV

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

overall_design: Refer to individual Series


title: Genome-wide study of HCFC1 binding sites and its associated transcription factors in cycling Human HeLa cells

summary: Analysis of transcriptional regulation in human cells has implicated a large number of promoter-specific DNA-binding proteins that regulate transcription via diverse mechanisms.  In some cases, these DNA-sequence-specific factors associate with intermediaries that orchestrate interactions with the chromatin-modifying enzymes.  One such intermediary is HCF-1 (host-cell factor-1; HCFC1).  HCF-1, first identified for its involvement in herpes-simplex virus transcription and subsequently shown to be an important cell-cycle regulator, has a poorly defined role in genome-wide transcriptional regulation.  We show here, by chromatin immunoprecipitation followed by high-throughput sequence analysis (ChIP-seq), that HCF-1 is a major transcriptional start site associated factor, whose promoter association correlates positively with transcriptional activity.  Thus, in HeLa cells HCF-1 is observed on 5400 generally active CpG-island promoters.  Examination of the DNA sequences underlying the HCF-1-binding sites revealed three sequence motifs associated with the binding of (i) ZNF143 and Ronin/THAP11, (ii) GABP, and (iii) YY1 sequence-specific transcription factors.  Subsequent ChIP-seq analysis of these four transcription factors revealed a large co-association of HCF-1 with these four transcription factors at approximately 90% of HCF-1-bound promoters.  These studies suggest that a relatively small number of transcription factors -- some (ZNF143 and Ronin/THAP11) in novel combinations -- play a major role in HeLa-cell transcriptional regulation in association with HCF-1.

overall_design: This experiment includes the sequencing data of material obtained from chromatin immunoprecipitation using antibodies against HCFC1(antibodies against the C-subunit and the N-subunit), PolII(antibody against the RPB2 subunit), H3K36ME3 and H3K4Me3 histone modifications, ZNF143, THAP11, GABPalpha and YY1. It also includes control data of the Input material. All of them were done using HeLa cycling cells.

first: Joëlle

last: Michaud

first: Viviane

last: Praz

first: Courtney

last: JnBaptiste

first: Winship

last: Herr


title: Genome-wide analysis of histone methylation reveals chromatin state-based regulation of host cellular gene expression induced by hepatitis B viruses


title: Expression changes in HeLa cells treated with siRNA against HCFC1 or control luciferase

summary: We compared in triplicate mRNA levels from cells treated with siRNA against either HCF-1 or, as a negative control, luciferase.  We observed that 19% of Refseq annotated genes are differentially expressed (either up or down regulated with a multiple testing corrected p value of ≤ 0.05) upon depletion of HCF-1.  This large number of differentially expressed genes upon HCF-1 depletion demonstrates a broad role of HCF-1 in the regulation of gene expression.

overall_design: The experiment includes biological triplicates of the expression changes between cycling HeLa cells treated with a control siRNA or siRNA against HCFC1.

first: Frédéric

last: Schütz


title: Molecular Rejuvenation of Gene Expression Pattern of Photoaged and Intrinsically Aged Human Skin by Broadband Light Treatment

status: Public on Jul 30 2012

city: Stanford

first: Kun

last: Qu

address: 269 Campus Dr. CCSR 2150

department: Dermatology

institute: Stanford University

summary: Studies in model organisms suggest that aged cells can be functionally rejuvenated, but whether this concept applies to human skin is unclear. Here we apply deep sequencing of RNA 3' ends ("3-seq") to discover the gene expression program associated with human photoaging and intrinsic skin aging (collectively termed "skin aging") and the impact of broadband light (BBL) treatment. We find that skin aging was associated with the significantly altered expression level of 2,265 coding and noncoding RNAs, of which 1,293 became "rejuvenated" after BBL treatment, i.e. more similar in expression level of youthful skin. Rejuvenated genes (RGs) included several known key regulators of organismal longevity and their proximal long non-coding RNAs. Skin aging is not associated with systematic changes in 3' end mRNA processing. Hence, BBL treatment can restore the gene expression pattern of photoaged and intrinsically aged human skin to resemble young skin. In addition, our data reveals a novel set of targets that may lead to new insights into the human skin aging process.

overall_design: Examination of broadband light treated and untreated human skin transcriptomes of 5 women aged 50 years or more. They were compared to the skin transcriptomes of 5 young women aged 30 years or less.

first: Anne

last: Chang

first: Patrick

last: Bitter

first: Meihong

last: Lin

first: Nicole

last: Rapicavoli

first: Howard

middle: Y


title: Effect of p53 knowkdown on genome-wide map of AR-DNA binding

city: Iowa City

first: Thomas

middle: B

last: Bair

state: IA

address: 335 EMRB

institute: University of Iowa

summary: We report that p53 knockdown changed AR-DNA binding across the genome. We found fewer AR-binding sites in the absence of p53.

overall_design: Examination of AR-DNA binding after p53 knockdown in LNCaP cells

first: Natalya

middle: V

last: Guseva

first: Oskar

last: Rokhlin

first: Rebecca

last: Glover

first: Michael

last: Cohen


title: The Translin-TRAX complex/C3PO is a ribonuclease in tRNA processing

city: Worcester

first: Craig

last: Mello

address: 368 Plantatoin Street, Suite AS5-2047

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

summary: The endogenous RNA substrates of Translin-TRAX complexes (also known as C3POs) and how they regulate diverse biological processes remain unknown. Here we show that Translin and TRAX do not play a significant role in RNAi in the filamentous fungus Neurospora crassa. Instead, the Neurospora C3PO complex functions as a ribonuclease that removes the 5’ pre-tRNA fragments after the processing of pre-tRNAs by RNase P. In translin and trax mutants, 5’ pre-tRNA fragments accumulate to very high levels that can be degraded specifically by both recombinant and endogenous Neurospora C3PO and recombinant Drosophila C3PO. In addition, the mutants have elevated tRNA levels and increased levels of protein translation and are more resistant to a programmed cell-death inducing agent. Together, this study identified the endogenous RNA substrates of C3PO and provides a potential explanation for its roles in seemingly diverse biological processes.

overall_design: Examine small RNA population changes in two different strain background

first: Liande

last: Li

first: Weifeng

last: Gu


title: X-linked H3K27me3 demethylase Utx is required for embryonic development in a sex-specific manner [ChIP-Seq data]

first: Albert

last: Cheng

summary: Embryogenesis requires the timely and coordinated activation of developmental regulators.  It has been suggested that the recently discovered class of histone demethylases (UTX and JMJD3) that specifically target the repressive H3K27me3 modification play an important role in the activation of “bivalent” genes in response to specific developmental cues. To determine the requirements for UTX in pluripotency and development, we have generated Utx null ES cells and mutant mice. The loss of UTX had a profound effect during embryogenesis. Utx null embryos had reduced somite counts, neural tube closure defects and heart malformation which presented between E9.5 and E13.5. Unexpectedly, homozygous mutant female embryos were more severely affected than hemizygous mutant male embryos. In fact, we observed the survival of a subset of UTX-deficient males which were smaller in size and had reduced life-span. Interestingly, these animals were fertile with normal spermatogenesis. Consistent with a mid-gestation lethality, UTX null male and female ES cells gave rise to all three germ layers in teratoma assays although sex-specific differences could be observed in the activation of developmental regulators in embryoid body assays. Lastly, ChIP-seq analysis revealed an increase in H3K27me3 in Utx null male ES cells. In summary, our data demonstrate sex-specific requirements for this X-linked gene while suggesting a role for UTY during development.

overall_design: Examination of H3K27me3 and H3K4me3 in UtxKO ES cells (V6.5 background) vs UtxFlx (V6.5 background) ES cells grown in LIF containing ES cell media or treated with retinoic acid without LIF.

first: Grant

last: Welstead

first: Rudolf

last: Jaenisch


title: Small RNA profiling of strains and lifecycle  of Chlamydomonas reinhardtii

first: Krys

last: Kelly

address: Downing Street

department: Plant Sciences

summary: High throughput sequencing was used to investigate the production of small RNAs from  in Chlamydomonas in different strains and different stages of the life cycle.  The association between these and methylation was assessed using  genomic sequencing, comparing a sequenced genome with one enriched for methylated DNA sequence by immuno-precipitation.

overall_design: Examination of small RNA production in several strains and of the methylation of regions producing these small RNAs.

first: Ruth

last: Dunn


title: A nuclear Argonaute promotes germline immortality and epigenetic inheritance across generations

city: Piscataway

first: Sam

middle: Guoping

state: NJ

address: Nelson Labs A125, 604 Allison Road

department: Molecular Biology and Biochemistry

institute: Rutgers University

summary: dsRNA-mediated gene silencing (RNAi) can be inherited for multiple generations in C. elegans. To understand this process we conducted a genetic screen for animals defective for transmitting RNAi silencing signals to future generations. This screen identified the gene heritable RNAi defective (hrde)-1. hrde-1 encodes an Argonaute (Ago) that associates with siRNAs in germ cells of the progeny of animals exposed to dsRNA. In nuclei of these germ cells, HRDE-1 engages the Nrde nuclear RNAi pathway to promote RNAi inheritance, and directs H3K9me3 chromatin marks at RNAi targeted genomic loci. Under normal growth conditions, HRDE-1 associates with endogenously expressed small RNAs, which direct nuclear gene silencing in germ cells. In RNAi inheritance mutant animals, silencing is lost over generational time. Concurrently, RNAi inheritance mutant animals exhibit progressively worsening germline defects that ultimately lead to sterility. These results establish that the Ago HRDE-1 directs gene-silencing events in germ cell nuclei, which are required for multi-generational RNAi inheritance and immortality of the germ cell lineage. We propose that C. elegans use the RNAi inheritance machinery to transmit epigenetic information, accrued by past generations, into future generations to ensure immortality of the germ cell lineage.

overall_design: H3K9me3 Chip-IP for C. elegans strains nrde-3, nrde-4, glp-4. Small RNA-seq for small RNAs co-immunoprecipitated with HRDE-1

first: Bethany

last: Buckley

first: Kirk

last: Burkhart

first: George

last: Spracklin

first: Aaron

last: Kershner

first: Heidi

last: Fritz

first: Judith

last: Kimble

first: Andrew

last: Fire

first: Scott

last: Kennedy


title: Plant Y-chromosome degeneration is retarded by haploid purifying selection.

city: Oxford

first: Dmitry

last: Filatov

address: South Parks Road

institute: University of Oxford

summary: Sex chromosomes evolved many times independently in many different organisms. According to the currently accepted model, X- and Y-chromosomes evolve from a pair of autosomes via a series of inversions leading to step-wise expansion of a non-recombining region on the Y chromosome (NRY) and the consequential degeneration of genes trapped in the NRY. Our results suggest that plants represent an exception to this rule due to their unique life-cycle that includes alteration of diploid and haploid generations and widespread haploid expression of genes in plant gametophytes. Using a new high-throughput approach we identified over 400 new genes expressed from X- and Y- chromosomes in Silene latifolia, a plant that evolved sex chromosomes about 10 million years ago. Y-linked genes show faster accumulation of amino-acid replacements and loss of expression, compared to X-linked genes. These degenerative processes are significantly less pronounced in more constrained genes and genes that are likely exposed to haploid-phase selection. This may explain why plants retain hundreds of expressed Y-linked genes despite millions of years of Y-chromosome degeneration, while animal Y-chromosomes are almost completely degenerate.

sample_organism:
Silene latifolia
Silene vulgaris

platform_organism:
Silene latifolia
Silene vulgaris

overall_design: We used a combination of Illumina sequencing of cDNA (RNAseq) and segregation analysis of SNPs identified from RNAseq to identify sex-linked genes in plant Silene latifolia. The experiment involved RNAseq from male and female parents and F1 progeny for two genetic crosses. We submit raw data in fastq format for 11 samples. Four of these samples are single end Solexa reads (a single file per sample) and seven samples were sequenced with paired end Solexa sequencing (two fastq files per sample) - 18 files in total.

first: M

last: Chibalina

first: D


title: Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling [TSS-Seq]

city: Ulsan

first: Donghyuk

last: Kim

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

department: Department of Chemical Engineering

country: South Korea

institute: UNIST

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of transcription start sites for two enterobacteria: Escherichia coli and Klebsiella pneumoniae.By obtaining over fourteen billion bases of sequence from 5' RACE (rapid amplification of cDNA ends) followed by deep sequencing, we generated genome-wide TSS (transcription start site) maps for those two species. With experimentally derived TSS datasets, we examined usage of multiple TSSs, length of 5' UTR (untranslated region), SD (Shine-Dalgarno) sequence motif, promoter sequence motif, and dinucleotide preference near TSS site. In addition, we used the TSS datasets to identify sRNAs (small RNAs) in E. coli and K. pneumoniae. Based on these analysis, we compared regulatory elements including promoter, 5' UTR and sRNAs between two species, and investigated similarities and differences of upstream regulatory regions. Moreover, sRNAs were also compared and analyzed in terms of their sequences and target sequences, presenting possible working mechanisms of K. pneumoniae sRNAs by transferring prior knowledge from E. coli sRNAs.

sample_organism:
Klebsiella pneumoniae
Escherichia coli K-12

overall_design: Examination of transcription start sites by biological duplicates from E. coli and K. pneumoniae

first: Jay

last: Hong

first: Bernhard

middle: O

last: Palsson


title: Cofactor-mediated Restriction of GATA-1 Chromatin Occupancy Coordinates Lineage-specific Gene Expression

first: Timothy

middle: Michael

last: Chlon

address: 3333 Burnet Ave

department: Oncology

institute: Cincinnati Children's


title: Dynamic Changes in Ezh2 Gene Occupancy Underlie Its Involvement in Neural Stem Cell Self-Renewal and Differentiation towards Oligodendrocytes

city: Boston

first: Falak

last: Sher

address: 3 Blackfan Circle, CLs 12220 Center for Life Science Building

department: F.M. Kirby Neurobiology Center

institute: CHB

summary:
BACKGROUND:
The polycomb group protein Ezh2 is an epigenetic repressor of transcription originally found to prevent untimely differentiation of pluripotent embryonic stem cells. We previously demonstrated that Ezh2 is also expressed in multipotent neural stem cells (NSCs). We showed that Ezh2 expression is downregulated during NSC differentiation into astrocytes or neurons. However, high levels of Ezh2 remained present in differentiating oligodendrocytes until myelinating. This study aimed to elucidate the target genes of Ezh2 in NSCs and in premyelinating oligodendrocytes (pOLs).
METHODOLOGY/PRINCIPAL FINDINGS:
We performed chromatin immunoprecipitation followed by high-throughput sequencing to detect the target genes of Ezh2 in NSCs and pOLs. We found 1532 target genes of Ezh2 in NSCs. During NSC differentiation, the occupancy of these genes by Ezh2 was alleviated. However, when the NSCs differentiated into oligodendrocytes, 393 of these genes remained targets of Ezh2. Analysis of the target genes indicated that the repressive activity of Ezh2 in NSCs concerns genes involved in stem cell maintenance, in cell cycle control and in preventing neural differentiation. Among the genes in pOLs that were still repressed by Ezh2 were most prominently those associated with neuronal and astrocytic committed cell lineages. Suppression of Ezh2 activity in NSCs caused loss of stem cell characteristics, blocked their proliferation and ultimately induced apoptosis. Suppression of Ezh2 activity in pOLs resulted in derangement of the oligodendrocytic phenotype, due to re-expression of neuronal and astrocytic genes, and ultimately in apoptosis.
CONCLUSIONS/SIGNIFICANCE:
Our data indicate that the epigenetic repressor Ezh2 in NSCs is crucial for proliferative activity and maintenance of neural stemness. During differentiation towards oligodendrocytes, Ezh2 repression continues particularly to suppress other neural fate choices. Ezh2 is completely downregulated during differentiation towards neurons and astrocytes allowing transcription of these differentiation programs. The specific fate choice towards astrocytes or neurons is apparently controlled by epigenetic regulators other than Ezh2.

overall_design: Examination of Ezh2 target sites in 2 different primary cells types

first: Erik

last: Boddeke

first: Marta

last: Olah

first: Sjef

last: Copray


title: HITS-CLIP analysis of FUS in lineage-committed cells.

status: Public on Jul 26 2012

city: Nagoya

first: Akio

last: Masuda

state: Aichi

address: 65 tsurumai-cho, Showa-ku

country: Japan

institute: Nagoya University Graduate School of Medicine

summary: In the present study, we performed HITS-CLIP analysis for FUS using mouse brain to extensively characterize tits RNA-binding sites and functional roles in RNA metabolisms. We identified preferential binding of FUS to stem-and-loop structures but without any discernible consensus motifs. FUS was preferentially bound to introns and 3' untranslated regions, but the exon/intron boundaries were mostly devoid of FUS-tags. Analysis of position-dependence of FUS-binding sites in regulating inclusion and skipping of exons disclosed that FUS is bound broadly around the alternatively spliced exons. Among them, however, noticeable CLIP-tags were observed in the downstream introns. We also noticed that FUS occasionally binds to the antisense strands in the promoter regions. Global analysis of CLIP-tags and expression profiles revealed that binding of FUS to the promoter antisense regions downgregulates transcription of the sense strand.

overall_design: HITS-CLIP (High Throughput Sequencing after Crosslinking and Immunoprecipitation) experiments targeting FUS in mouse cerebrums derived from 12-week-old C57BL/6 mice

first: Kinji

last: Ohno


title: RNA-seq from ENCODE/Stanford/Yale

status: Public on Jul 25 2012

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Philip Cayting mailto:pcayting@stanford.edu). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu).

The tracks show enrichment of RNA sequence tags mapped to the mouse genome generated by high throughput sequencing (RNA-Seq). Double stranded cDNA was synthesized from enriched RNA that was obtained after depletion of ribosomal RNA. Pieces of cDNA, 300-350 nucleotides in length, were PCR amplified, adapter ligated, and sequenced on an Illumina HiSeq sequencer.

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

overall_design: Cells were grown according to the approved ENCODE cell culture protocols (http://hgwdev.cse.ucsc.edu/ENCODE/protocols/cell). Total RNA was extracted using RNeasy Mini Kit (74104, Aiagen), following the manufacturer's protocol. Ribosomal RNA was removed from total RNA using the Ribo-ZeroTM Gold Kits (MRZG126, Epicentre). Double-stranded cDNA synthesis was performed on the rRNA depleted RNA using random primers and the SuperScript double-stranded cDNA synthesis kit (11917-010, Life Tech). After first strand cDNA synthesis, NucAway Spin Column (Ambion cat. 100070-30) was used to remove dNTPs. In the second strand cDNA synthesis reaction, dTTP in the dNTP mix was substituted with dUTP. After end repair and addition of 'A' base to 3' end, illumina paired-end adapter was ligated to Double-stranded cDNA library. After gel size selection of adapter ligated cDNA (300-350), Uracil-N-Glycosylase (UNG: Applied Biosystems) was used to digest the second strand cDNA (Parkhomchuk et al. , 2009). PCR amplified adapter ligated cDNA was sequenced using Illumina HiSeq. Sequence reads of 2x101 nt long with 0-2 mismatches were mapped to the mouse genome (version mm9) using the BWA aligner, version 0.5.7. The signal height corresponds to the number of overlapping fragments at each nucleotide position in the genome.

first: Michael

last: Snyder

first: Philip

last: Cayting


title: small RNA discovery in fission yeast Schizosaccharomyces japonicus

city: Huddinge

first: Agata

last: Smialowska

address: Halsovagen 7

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

summary: We used massively parallel sequencing to discover and characterize small RNAs (sRNAs) from fission yeast Schizosaccharomyces japonicus. We found that, unlike in related S. pombe, a substantial fraction of sRNAs maps to transposons, both telomeric and centromeric.

overall_design: small RNA library from total RNA isolations from Schizosaccharomyces japonicus

first: Karl

last: Ekwall


title: Genome-wide analysis of the role of FOG-1 in GATA-1 chromatin occupancy

summary: We report ChIP-Seq data for GATA-1 and the FOG-binding mutant of GATA-1 (GATA-1^V205G) in G1ME cells, a Gata1-null cell line with both erythroid and megakaryocytic differentiation potential.  We introduced HA-tagged GATA-1 or V205G into G1ME cells via retroviral transduction.  The cells were crosslinked at 48h post-transduction, and an HA antibody was used for chromatin immunoprecipitation (ChIP).  ChIP and input samples were sequenced on Illumina GAII high-throughput sequencer.  The data reveal GATA-1-specific and V205G-specific bidning sites, indicating that FOG-1 both faacilitates and prohibits GATA-1 chromatin occupancy in a context-dependent manner.

overall_design: Examinaton of chromatin occupancy of GATA-1 anda FOG-binding mutant of GATA-1 in G1ME cells cultured in TPO.

first: Louis

last: Dore

first: John

last: Crispino


title: Global identification and characterization of intermediate-size non-coding RNAs in Oryza sativa

status: Public on Jul 27 2012

city: Beijing

first: Wei

last: Chen

address: No.5 Yiheyuan Road

institute: Peking University

summary: In this study, we employed a special size fractionation and cDNA library construction method followed by 454 deep sequencing to systematically profile rice intermediate-size ncRNAs. Our analysis resulted in the identification of 1349 ncRNAs in total, including 754 novel ncRNAs of an unknown functional category. Chromosome distribution of all identified ncRNAs showed no strand bias, and displayed a pattern similar to that observed in protein-coding genes with few chromosome dependencies. More than half of the ncRNAs were centered around the plus-strand of the 5’ and 3’ termini of the coding regions. The majority of the novel ncRNAs were rice specific, while 78% of the small nucleolar RNAs (snoRNAs) were conserved. Tandem duplication drove the expansion of over half of the snoRNA gene families. Furthermore, 90% of the snoRNA candidates were shown to produce small RNAs between 20-30 nt, 80% of which were associated with ARGONAUT proteins generally, and AGO1b in particular. Overall, our findings provide a comprehensive view of an intermediate-size non-coding transcriptome in a monocot species, which will serve as a useful platform for an in-depth analysis of ncRNA functions.

overall_design: Examination of non-coding RNA in 2 stages in Oryza sativa, using 454 deep sequecing

first: Tingting

last: Liu


title: Nucleosome dynamics specifies genome-wide binding of the male germ cell gene regulator CTCFL and of CTCF [ChIP-Seq]

city: Rotterdam

first: frank

last: sleutels

address: Dr Molewaterplein 50

department: cell biology and genetics

country: Netherlands

institute: ErasmusMC

summary: CTCF and CTCFL DNA binding profile in CTCFL induced and non-induced ES cells.CTCF is a highly conserved and essential zinc finger protein that in conjunction with cohesin organizes chromatin into loops, thereby regulating gene expression and epigenetic events. The function of CTCFL or BORIS, the testis-specific paralogue of CTCF, is less clear. Here, we show that CTCFL is only transiently present during spermatogenesis, prior to the onset of meiosis, when the protein co-localizes in nuclei with ubiquitously expressed CTCF. Our data show that CTCFL is functionally different from CTCF and its absence in mice causes sub-fertility due to a partially penetrant testicular atrophy. Genome-wide studies reveal that CTCFL and CTCF bind similar consensus sequences. However, only ~2000 out of the ~5,700 CTCFL and ~31,000 CTCF binding sites overlap. CTCFL binds promoters with loosely assembled nucleosomes, whereas CTCF favors consensus sites surrounded by phased nucleosomes. Thus, nucleosome dynamics specifies the genome-wide binding of CTCFL and CTCF. We propose that the transient expression of CTCFL in spermatogonia and preleptotene spermatocytes serves to occupy a subset of promoters and maintain the expression of male germ cell genes

overall_design: ChIP-seq for CTCF (with CTCF antibody) and CTCFL (with V5 antibody) in CTCFL_V5_GFP induced and non-induced ES cells

first: Frank

last: Sleutels

first: Widia

last: Soochit

first: Marek

last: Bartkuhn

first: Helen

last: Heath

first: Sven

last: Dienstbach

first: Philipp

last: Bergmaier

first: Vedran

last: Franke

first: Manuel

last: Rosa-Garrido

first: Suzanne

last: van de Nobelen

first: Lisa

last: Caesar

last: van der Reijden

first: Jan

last: Christian Bryne

first: Wilfred

last: van Ijcken

first: J

last: Grootegoed

first: M

middle: D

last: Delgado

first: Boris

last: Lenhard

first: Rainer

last: Renkawitz

last: Grosveld

first: Niels

last: Galjart


title: The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments

city: Berkeley

first: Nicholas

middle: T

last: Ingolia

email: ingolia@berkeley.edu, nick@ingolia.org

address: 1 Barker Hall # 3202

department: Molecular and Cell Biology

institute: University of California, Berkeley

summary: Recent studies highlight the importance of translational control in determining protein abundance, underscoring the value of measuring gene expression at the level of translation. We present a protocol for genome-wide, quantitative analysis of in vivo translation by deep sequencing. This ribosome profiling approach maps the exact positions of ribosomes on transcripts by nuclease footprinting. The nuclease-protected mRNA fragments are converted into a DNA library suitable for deep sequencing using a strategy that minimizes bias. The abundance of different footprint fragments in deep sequencing data reports on the amount of translation of a gene. Additionally, footprints reveal the exact regions of the transcriptome that are translated. To better define translated reading frames, we describe an adaptation that reveals the sites of translation initiation by pre-treating cells with harringtonine to immobilize initiating ribosomes. The protocol we describe requires 5 - 7 days to generate a completed ribosome profiling sequencing library.

overall_design: Ribosome profiling in cultured mammalian cells under three different footprinting conditions

first: Gloria

last: Brar

first: Silvi

last: Rouskin

first: Anna

last: McGeachy

first: Jonathan

last: Weissman


title: Sequencing random oligonucleotides using standard GA II protocol

status: Public on Jul 23 2012

first: Helio

last: Pais

address: Jonh Radcliffe Hospital

department: Weatherall Institute of Molecular Medicine

summary: Study on sequencing biases introduced by library preparation step, namely by ligases. Comparison between standard Illumina protocol and improved High Definition (HD) protocol.

overall_design: Four replicates for N21 (21 random nucleotides), one replicate for N9 (9 random nucleotides), using either standard Illumina protocol or HD protocol

first: Karim

last: Sorefan

first: Vincent

last: Moulton

first: Tamas

last: Dalmay


title: Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

status: Public on Jul 22 2012

city: Stockholm

first: Daniel

last: Ramsköld

address: Nobels väg 3

institute: Karolinska Institutet

summary: We assessed Smart-Seq, a new single-cell RNA-Seq library preparation method, on a variety of mouse and human RNA samples or cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We generated RNA-Seq libraries for dilution series of MAQC reference RNA and mouse brain RNA to assess technical reproducibility, and for a variety of individual cells including putative circulating tumour cells.

first: Shujun

last: Luo

first: Yu

middle: C

last: Wang

first: Louise

last: Laurent

first: Rickard

last: Sandberg

first: Gary

middle: P

last: Schroth


title: Idh1-R132H mutation increases murine hematopoietic progenitors and alters epigenetics.

city: Miami

first: Maria

middle: Eugenia

last: Figueroa

state: FL

address: 1501 NW 10th Ave, BRB 709A, Locator code C227

institute: University of Miiami

summary: Mutations in the IDH1 and IDH2 genes encoding isocitrate dehydrogenases are frequent in human glioblastomas1 and cytogenetically normal acute myeloid leukemias (AML)2. These alterations are gain-of-function mutations in that they drive the synthesis of the “oncometabolite” R-2-hydroxyglutarate (2HG)3. It remains unclear how IDH1 and IDH2 mutations modify myeloid cell development and promote leukemogenesis. Here we report the characterization of conditional knock-in mice in which the most common IDH1 mutation, Idh1-R132H, is inserted into the endogenous murine Idh1 locus and is expressed in cells of the hematopoietic (Vav-KI) or more specifically in cells of the myeloid (LysM-KI) lineage. These mutants show increased numbers of early hematopoietic progenitors and develop splenomegaly and anemia with extramedullary hematopoiesis, suggesting a dysfunctional bone marrow niche. Furthermore, LysM-KI cells exhibit both hypermethylated histones and changes to DNA methylation similar to those observed in human IDH1/2-mutant AML. Thus, our study is the first to describe the generation of conditional Idh1-R132H-KI mice. Furthermore, our study is also the first report showing the induction of a leukemic DNA methylation signature in a modeled system and sheds light on the mechanistic links between IDH1 mutation and human AML.

overall_design: DNA methylation profiling in LSK cells from IDH1-R132H knock-in mice vs. control mice

first: Masato

last: Sasaki

first: Christiane

last: Knobbe

first: Tak

last: Mak

middle: E

first: Ari

last: Melnick


title: RNA-seq from ENCODE/UW

status: Public on Jul 20 2012

first: ENCODE

last: DCC

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

This track was produced as part of the mouse ENCODE Project. This track shows RNA-seq measured genome-wide in mouse tissues and cell lines (http://hgwdev.cse.ucsc.edu/cgi-bin/hgEncodeVocab?type=cellType). Poly-A selected mRNA was used as the source for transcriptome profiling of tissues and cell types that also had corresponding DNase I hypersensitive profiles.

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

overall_design:
Cells were grown according to the approved ENCODE cell culture protocols. Fresh tissues were harvested from mice and stored until used for preparing total RNA samples. The total RNA was used as starting material to select poly-A RNA and used for constructing SOLiD libraries according to the protocols supplied by the manufacturer. All RNA samples were spiked in with NIST standards before libraries were constructed. The RNA-seq libraries were sequenced on ABI SOLiD sequencing platform as 50-base reads according to the manufacturer's recommendations.
Reads were aligned to the mm9 reference genome using ABI BioScope software version 1.2.1. Colorspace FASTQ format files were created using Heng Li's solid2fastq.pl script version 0.1.4 (Li et al., 2009a), representing 0, 1, 2, 3 color codes with the letters A, C, G, T respectively. Signal files were created from the BAM (Li et al., 2009b) alignments using BEDTools (Quinlan et al., 2010).

first: Richard

last: Sandstrom


title: Composition and organization of active centromere sequences in complex genomes

city: Durham

first: Karen

middle: Elizabeth

last: Hayden

state: NC

address: 101 Science Drive

department: Institute for Genome Sciences and policy

institute: Duke University

summary: We report the sequences bound to CENP-A in the dog genome (Canis familiaris) for high-throughput characterization of centromeric sequences. We compare these ChIPSeq reads (72 bp, single read) against a reference centromeric satellite DNA domain database for the dog genome, resulting in the annotation of sequence variation and estimated abundance of seven satellite families together with adjacent, non-satellite sequences.  To study global patterns of sequence diversity and characterizing the subset of sequences correlated with centromere function, these sequences were evaluated relative to a comprehensive centromere sequence domain k-mer library.  From this analysis, we identify functional sequence features from two satellite families (CarSat1 and CarSat2) that are defined by distinct arrays subtypes.

overall_design: Sequences bound to CENP-A in MDCK (dog) cell line

first: Huntington

middle: F

last: Willard


title: Target RNA repertoire of mouse Mili and Miwi proteins reveals piRNA biogenesis and Miwi function in spermiogenesis

city: Wilmington

first: Qi

last: Zheng

state: DE

address: 1701 Rockland Road

institute: Nemours Children's Health

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

overall_design: Refer to individual Series


title: Nucleosome dynamics specifies genome-wide binding of the male germ cell gene regulator CTCFL and of CTCF

first: frank

last: sleutels


title: 5-hmC in the brain: abundance in synaptic genes and differences at the exon-intron boundary

status: Public on Aug 24 2012

city: Toronto

first: Shraddha

last: Pai

state: ON

address: 160 College Street, Room 602

institute: University of Toronto

type: Methylation profiling by genome tiling array


title: Target RNA repertoire of mouse Mili and Miwi proteins reveals piRNA biogenesis and Miwi function in spermiogenesis [HITS-CLIP]

summary: Germ cells employ elaborate mechanisms to maintain and protect their genetic material, and also to regulate gene expression during the complex differentiation process of gametogenesis. Piwi proteins, a subclade of the Argonaute family, are expressed mainly in the germline and bind piRNAs, a novel and diverse class of small RNAs whose biogenesis and putative functions are still largely elusive. We employed High Throughput Sequencing after Crosslinking and Immunoprecipitation (HITS-CLIP) coupled with RNA-Seq to characterize the genome-wide target RNA repertoire of Mili and Miwi, two mouse Piwi proteins. Our analysis outlines a model for primary piRNA biogenesis in postnatal mouse and indicates that piRNAs do not mediate target RNA recognition, but rather are the end products of RNA processing. Moreover, we identify a set of mRNAs essential for spermiogenesis that are bound and regulated by Miwi, directly implicating Piwi proteins in the control of gene expression at key time points of spermiogenesis.

overall_design: HITS-CLIP (High Throughput Sequencing after Crosslinking and Immunoprecipitation) experiments targeting two mouse Piwi proteins Mili and Miwi.

first: Anastassios

last: Vourekas

first: Panagiotis

last: Alexiou

first: Manolis

last: Maragkakis

first: Yohei

last: Kirino

first: Brian

last: Gregory

first: Zissimos

last: Mourelatos


title: Gene expression in attached vs. released collagen matrices populated with human foreskin fibroblasts

city: Omaha

first: Mark

middle: A.

last: Carlson

address: Surgery 112, VA Medical Center, 4101 Woolworth Ave

department: Surgery

institute: Univ Nebraska Med Ctr

summary: The fibroblast-populated 3D collagen matrix has been used to study the effect of mechanical stress on cell fate; this process is relevant to the fields of wound healing and tissue engineering. Gene array data was generated from mechanically stressed vs. stress-released matrices. The parameters of the collagen matrix model were: collagen type = bovine type I; collagen concentration = 1.5 mg/mL; initial matrix volume = 0.2 mL; initial matrix diameter = 11 mm (cultured in 24-well plates); cell type = human foreskin fibroblast, passage <10; initial matrix cell concentration = 1,000,000 cell/mL (200,000 cell/matrix); culture medium = 5% FBS in DMEM with 1 µg/mL ascorbate. Matrices (n = 6 per experimental group) were incubated for 24 hr in the attached state; the released groups then underwent matrix detachment from the culture plate (defined as t = 0), while the attached groups were left undisturbed. RNA was isolated from attached and released matrices 6 and 24 hr after t = 0. Gene expression in the attached vs. released condition at 6 or 24 hr then was analyzed by hybridizing the anti-sense RNA derived from attached and released matrices at a given time point onto a single chip.

overall_design: Refer to the attached Figure 1 for the experimental design. The index experiment was defined as the comparison of gene expression in attached vs. released collagen matrices in a single strain of human foreskin fibroblasts at 6 and 24 hr after stress-release (i.e., after t = 0). Each experiment utilized two mechanical conditions (attached and released) at two time points (6 and 24 hr). So with each condition utilizing 6 matrices, each index experiment required a total of 24 matrices. In each index experiment, the chip hybridizations were: (i) 6 hr attached vs. 6 hr released, and (ii) 24 hr attached vs. 24 hr released (i.e., two gene chips per index experiment). Each hybridization was done using a 10K spotted gene chip manufactured in the UNMC Microarray Core Facility. The index experiment was performed on three fibroblast strains, meaning that expressional data was derived from three foreskin donors (nonpooled samples). Dye-swap was not performed; dye assigned to attached vs. released remained constant among all chips. Since the index experiment was performed three times, the total number of gene chips used for this entire dataset was six.

middle: A

first: James

last: Eudy

first: Lynette

last: Smith

first: Jeremiah

middle: J

last: Gums


title: Target RNA repertoire of mouse Mili and Miwi proteins reveals piRNA biogenesis and Miwi function in spermiogenesis [RNA-Seq]

overall_design: Directional RNA-seq experiments of 5 time-points during mouse postnatal testis development


title: Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling

first: Donghyuk

last: Kim

sample_organism: Klebsiella pneumoniae subsp. pneumoniae MGH 78578


title: Chromatin Interactions by 5C from ENCODE/Dekker Univ. Mass.

status: Public on Jul 19 2012

city: Stanford

first: ENCODE

last: DCC

summary:
Amartya Sanyal mailto:amartya.sanyal@umassmed.edu (Wet Lab), Bryan R. Lajoie mailto:bryan.lajoie@umassmed.edu, Gaurav Jain mailto:gaurav.jain@umassmed.edu (Dry Lab), Job Dekker mailto:job.dekker@umassmed.edu (Principal Investigator)

This track contains chromatin interaction data generated using the 5C (Chromatin Conformation Capture Carbon Copy) method by the ENCODE group (Dekker Lab) located at the University of Massachusetts, Worcester, MA. This track shows the significant looping interactions between transcriptional start sites (TSS) and distal regulatory elements in the context of the 44 ENCODE pilot regions spanning 1% of the human genome.
Although the DNA is a linear sequence, the chromatin, which is packed and organized inside the nucleus, does not function linearly. This is most clearly illustrated by the fact that genes are often regulated by elements that are located hundreds of kilobases away in the linear genome. Imaging techniques have shown that regulatory elements can act over large genomic distances by engaging in direct physical interactions with target genes, resulting in the formation of chromatin loops. Based on these observations, we have envisaged that the spatial organization of the genome resembles a three-dimensional network that is driven by physical associations between genes and regulatory elements, both in cis (within the same chromosome) and in trans (between different chromosomes) (Dekker, 2006).
Apart from imaging technology which is labor intensive and low-throughput, long-range chromatin looping interactions can be detected using the Chromosome Conformation Capture (3C) technology (Dekker et al., 2002). The 3C method employs formaldehyde cross-linking to covalently link interacting chromatin segments in intact cells. Cells are subsequently lysed and chromatin is digested with a restriction enzyme of choice. The digested fragments are then ligated under dilute conditions to facilitate intramolecular ligation. The result is a genome-wide interaction library of ligation products corresponding to all possible chromatin interactions. Specific ligation products can then be detected by PCR using specific primer pairs.
The 5C method was developed to dramatically increase 3C throughput (Dostie et al., 2006; Dostie and Dekker, 2007). The 5C method greatly increases the scale of chromatin interaction detection by replacing the PCR detection step of 3C with ligation-mediated amplification (LMA). LMA is advantageous due to a much higher level of multiplexing by using thousands of primers in a single reaction to detect millions of chromatin interactions (ligation junctions) in parallel. The LMA step effectively "copies" 3C ligation products into much smaller 5C ligation products that precisely correspond to ligation junctions formed during the 3C procedure. The products of the multiplexed LMA reaction constitute the 5C library. The composition of the 5C library is determined using high-throughput DNA sequencing.

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

overall_design:
The aim of the pilot study was to generate a "connectivity map" between transcription start sites (TSS) and distal regulatory elements within the 44 ENCODE PILOT regions.
In the current scheme, 5C primers were designed for all HindIII restriction fragments. Reverse primers were designed on fragments containing the TSS of annotated genes. Forward primers were designed on all other fragments. This design allowed for the interrogation of all TSS with all other restriction fragments, thus generating an interaction map between TSS and regulatory elements. For gene desert ENCODE pilot regions (for example ENr313), an altered scheme of forward and reverse primers was designed.
Primers were selected for relative uniqueness using a custom 15-mer frequency table and BLAST. A custom hexamer barcode was added to each primer to ensure the sequence was unique relative to the primer pool being used. Primers were also selected for the appropriate melting temperature and GC-content and a universal tail sequence for amplification.
The 44 ENCODE regions were analyzed in two groups using two separate 5C primer pools. The first group (ENm) contained the manually-picked ENCODE regions, ENm001-014 and ENr313. The second group (ENr) contained the 30 randomly-picked ENCODE regions. The two 5C primer pools were made by pooling 5C primers for interrogating long-range interactions in the two groups of ENCODE regions. The primer pool for the ENm group contained a total of 3,150 primers (476 reverse 5C primers and 2674 forward 5C primers). This primer pool allowed interrogation of a total of 1,272,824 interactions. Of these, 83,427 interactions were between fragments that were both located in the same ENCODE region. This primer pool for the ENr group contained a total of 3,152 primers (505 reverse 5C primers and 2647 forward 5C primers). This primer pool allowed interrogation of a total of 1,336,735 interactions. Of these, 34,859 interactions were between fragments that were both located in the same ENCODE region. In total, 981 reverse primers and 5,321 forward primers were designed (corresponding to ~77.1% (6,302/8,174) of all HindIII fragments in the 44 ENCODE regions).
Currently, data for two biological replicates have been generated for ENCODE Tier I (GM12878 and K562), Tier II (HeLa-S3), and H1 human embryonic stem cells (H1-hESC), spanning 14 ENCODE manual regions along with one random region (ENr313) as well as 30 random regions separately using high-throughput paired-end sequencing in the Illumina GA2 platform. The looping interactions, which are detected in both the biological replicates, are considered significant.

first: Amartya

last: Sanyal

first: Bryan

last: Lajoie

first: Gaurav

last: Jain

first: Job

last: Dekker


title: Chromatin based modeling of transcription rates identifies the contribution of different regulatory layers to steady-state mRNA levels

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

institute: Friedrich Miescher Institute for Biomedical Research

summary: Messenger RNA levels in eukaryotes are balanced by two consecutive regulatory layers. Primary, transcriptional regulation at the level of chromatin and secondary, post-transcriptional regulation of the initial transcript in the cytoplasm. Each layer is individually studied in mechanistic detail, while integration of both processes is required to quantify the individual contribution to steady-state RNA levels. Here we show that chromatin features are sufficient to model transcription rate but with different sensitivities in dividing versus post mitotic cells. In both cases chromatin derived transcript levels explains over 80% of variance in measured RNA level enabling to separate transcription from different post-transcriptional processes. By further inclusion of measurements of mRNA half-life and micro RNA expression data we identify a low quantitative contribution of RNA decay by either micro RNA or general differential turnover to final mRNA levels. Together this establishes a chromatin based quantitative model for the contribution of transcriptional and posttranscriptional processes to steady-state levels of messenger RNA.

overall_design:
H3K36me3 ChIP followed by deep sequencing // time-series of mRNA measurement on Affymetrix microarray platform following actinomycinD treatment.
MmES Samples: mRNA measurement on Affymetrix microarray platform following thioU labeling and separation of fractions according to labeled (newly synthetised) and unlabeled (pre-existing) RNA.

first: Sylvia

last: Tippmann

first: Robert

last: Ivanek

first: Dimos

last: Gaidatzis

first: Anne

last: Schöler

first: Erik

last: van Nimwegen

first: Peter

last: Stadler

first: Michael

last: Schübeler