title: Genome-wide DNA methylation patterns and its correlation with gene expression profile in Nasonia vitripennis

city: Ithaca

first: Andrew

last: Clark

address: 227 Biotech Building

institute: Cornell University

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: seq-SDQ2366_MRE11_FEM2_AD

status: Public on Aug 28 2013

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: Genome binding/occupancy profiling by high throughput sequencing

summary:
modENCODE_submission_5193
This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents. We will integrate information generated with existing knowledge on the biology of the targets and perform ChIP-seq analysis on mutant and RNAi extracts lacking selected target proteins.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: fem-2(b245); Developmental Stage: Germline containing young adult; Genotype: fem-2(b245)III; Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage Germline containing young adult; temp (temperature) 20 degree Celsius; Strain fem-2(b245); Antibody MRE-11 SDQ2366 (target is MRE-11)

first: Abby

last: Dernburg

first: Christina

last: Whittle


title: seq-HK00012_H3K36me2_2C3_N2_Eemb

summary:
modENCODE_submission_5164
This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include key histone modifications and histone variants. We will integrate information generated with existing knowledge on the biology of the targets and perform ChIP-seq analysis on mutant and RNAi extracts lacking selected target proteins.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Early Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  EXPERIMENTAL FACTORS: Developmental Stage Early Embryo; temp (temperature) 20 degree celsius; Strain N2; Antibody HK00012 H3K36me2:2C3 (target is H3K36me2)

first: Susan

last: Strome

first: Thea

last: Egelhofer

first: Andreas

last: Rechtsteiner


title: Progesterone Receptor Targetome in the Mammary Gland

status: Public on Aug 27 2013

city: Houston

first: Ashlee

middle: Renae

last: Lain

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

country: USA

institute: Baylor College of Medicine


title: Progesterone receptor ChIP-seq within the mouse mammary gland

summary: Progesterone (P) acting through its cognate nuclear receptors (PRs) plays an essential role in driving pregnancy-associated branching morphogenesis of the mammary gland. However, the fundamental mechanisms, including global cistromic and acute genomic transcriptional responses that are required to elicit active branching morphogenesis in response to P, have not been elucidated. We used chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) to identify P-regulated genes that directly recruit PRs in the mouse mammary gland after acute P treatment.

overall_design: Two replicate PR ChIP samples and two replicate input DNA control samples from mouse mammary glands after mice are treated subcutaneously with 17β-Estradiol for 24 hours and then 17β-Estradiol plus Progesterone for 6 hours.

middle: R

first: Chad

middle: J

last: Creighton

first: Orla

middle: M

last: Conneely


title: A long noncoding RNA mediates both activation and repression of immune response genes.

status: Public on Aug 26 2013

city: Worcester

first: Daniel

last: Aiello

state: ma

address: 364 plantation Street

department: Division of Infectious Diseases and Immunology, Department of Medicine

institute: UMASS Medical School

type: Expression profiling by high throughput sequencing

summary: An inducible program of inflammatory gene expression is central to antimicrobial defenses. This response is controlled by a collaboration involving signal-dependent activation of transcription factors, transcriptional co-regulators, and chromatin-modifying factors. We have identified a long noncoding RNA (lncRNA) that acts as a key regulator of this inflammatory response. Pattern recognition receptors such as the Toll-like receptors induce the expression of numerous lncRNAs. One of these, lincRNA-Cox2, mediates both the activation and repression of distinct classes of immune genes. Transcriptional repression of target genes is dependent on interactions of lincRNA-Cox2 with heterogeneous nuclear ribonucleoprotein A/B and A2/B1. Collectively, these studies unveil a central role of lincRNA-Cox2 as a broad-acting regulatory component of the circuit that controls the inflammatory response

overall_design: Examination of Mus musculus (C57BL/6 background) gene expression changes following stimulation with Pam3Cys4 in presence or absence of shRNA specifically targetting lncRNA-COX2

last: Carpenter

first: Katherine

middle: A

last: Fitzgerald

first: D

last: Caffrey


title: Base-pair level resolution of the Nasonia vitripennis methylome

summary: The parasitoid wasp Nasonia vitripennis is an emerging genetic model for functional analysis of DNA methylation. Here, we characterize genome-wide methylation at a base-pair resolution, and compare these results to gene expression across five developmental stages and to methylation patterns reported in other insects. An accurate assessment of DNA methylation across the genome is accomplished using bisulfite sequencing of adult females from a highly inbred line. One-third of genes show extensive methylation over the gene body, yet methylated DNA is not found in non-coding regions and rarely in transposons. Methylated genes occur in small clusters across the genome. Methylation demarcates exon-intron boundaries, with elevated levels over exons, primarily in the 5’ regions of genes. It is also elevated near the sites of translational initiation and termination, with reduced levels in 5’ and 3’ UTRs. Methylated genes have higher median expression levels and lower expression variation across development stages than non-methylated genes. There is no difference in frequency of differential splicing between methylated and non-methylated genes, and as yet no established role for methylation in regulating alternative splicing in Nasonia. Phylogenetic comparisons indicate that many genes maintain methylation status across long evolutionary time scales. Nasonia methylated genes are more likely to be conserved in insects, but even those that are not conserved show broader expression across development than comparable non-methylated genes. Finally, examination of duplicated genes shows that those paralogs that have lost methylation in the Nasonia lineage following gene duplication evolve more rapidly, show decreased median expression levels, and increased specialization in expression across development. Methylation of Nasonia genes signals constitutive transcription across developmental stages, whereas non-methylated genes show more dynamic developmental expression patterns. We speculate that loss of methylation may result in increased developmental specialization in evolution and acquisition of methylation may lead to broader constitutive expression.

overall_design: Whole-genome bisulfite sequencing of 24-hour adult female Nasonia vitripennis whole body samples using Iilumina GAIIx and HiSeq2000.

first: John

middle: H

last: Werren

middle: G

first: Xu

last: Wang


title: CHD5 is required for neurogenesis and has a dual role in facilitating gene expression and Polycomb gene repression

city: Dublin

first: Adrian

middle: P.

last: Bracken

address: 1 Lincoln Place

department: Department of Genetics

country: Ireland

institute: Trinity College Dublin

summary: The chromatin remodeler CHD5 is expressed in neural tissue and is frequently deleted in aggressive neuroblastoma. Very little is known about the function of CHD5 in the nervous system or its mechanism of action. Here we report that depletion of Chd5 in the developing murine neocortex blocks neuronal differentiation and leads to an accumulation of undifferentiated progenitors. CHD5 binds a large cohort of genes and is required for facilitating the activation of neuronal genes. It also binds a cohort of Polycomb targets and is required for the maintenance of H3K27me3 on these genes. Interestingly, the chromodomains of CHD5 directly bind H3K27me3 and are required for neuronal differentiation. In the absence of CHD5, a subgroup of Polycomb-repressed genes becomes aberrantly expressed. These findings provide new insights into the regulatory role of CHD5 during neurogenesis and suggest how inactivation of this candidate tumor suppressor might contribute to neuroblastoma.

overall_design: Examination of genome-wide binding/occupancy of CHD5 in the SH-SY5Y cell line

first: Chris

last: Egan

middle: P


title: Unlock the mystery of the hard-to-sequence phage genome: discovering a novel mechanism of bacterial immunity

status: Public on Aug 22 2013

city: Chongqing

first: Shuguang

last: Lu

address: 30# Gaotanyan St., Shapingba District,

department: Department of Microbiology

country: China

institute: Third Military Medical University

summary: Whole-genome sequencing is an important way to understand the genetic information, gene function, biological characteristics, and living mechanisms of organisms. There is no difficulty to have mega-level genomes sequenced at present. However, we encountered a hard-to-sequence genome of Pseudomonas aeruginosa phage PaP1. The shotgun sequencing method failed to dissect this genome. After insisting for 10 years and going over 3 generations of sequencing techniques, we successfully dissected the PaP1 genome with 91,715 bp in length. Single-molecule sequencing revealed that this genome contains lots of modified bases, including 51 N6-methyladenines (m6A) and 152 N4-methylcytosines (m4C). At the same time, further investigations revealed a novel immune mechanism of bacteria, by which the host bacteria can recognize and repel the modified bases containing inserts in large scale, and this led to the failure of the shotgun method in PaP1 genome sequencing. Strategy of resolving this problem is use of non-library dependent sequencing techniques or use of the nfi- mutant of E. coli DH5α as the host bacteria to construct the shotgun library. In conclusion, we unlock the mystery of phage PaP1 genome hard to be sequenced, and discover a new mechanism of bacterial immunity in present study.

overall_design: Methylation profiling of Pseudomonas aeruginosa phage PaP1 using kinetic data generated by single-molecule, real-time (SMRT) sequencing on the PacBio RS.

first: Shuai

last: Le

first: Yinling

last: Tan

first: Ming

last: Li

first: Chang

last: Liu

first: Kebin

last: Zhang

first: Jianjun

last: Huang

first: Haimei

last: Chen

first: Xiancai

last: Rao

first: Junmin

last: Zhu

first: Lingyun

last: Zou

first: Qingshan

last: Ni

first: Shu

first: Jing

first: Xiaolin

last: Jin

first: Qiwen

last: Hu

first: Xia

last: Zhao

first: Lin

first: Guangtao

first: Fuquan


title: H4K16 acetylation marks active genes and enhancers of embryonic stem cells, but does not alter chromatin compaction (I) [ChIP-Seq]

status: Public on Aug 23 2013

city: Edinburgh

first: Gillian

last: Taylor

address: MRC HGU Crewe Road South

country: United Kingdom

institute: IGMM

summary: We report that acetylation of H4K16 is a new marker of active enhancers and that some enhancers are marked by H3K4me1, MOF and H4K16ac but not by acetylated H3K27 or p300, suggesting that they are novel p300-independent regulatory elements.

overall_design: ChIP-seq for H4K16 acetylation in undifferentiated ES cells, and cells after 3 days of retinoic acid differentiation, along with MNase digested input for both samples

first: Ragnhild

last: Eskeland

first: Madapura

last: Pradeepa

first: Wendy

last: Bickmore


title: Redistribution of the Lamin B1 genomic binding profile affects spatial rearrangement of heterochromatic domains and gene expression during senescence

city: Cambridge

first: Rafik

last: Salama

address: Li Ka Shing Centre, Robinson Way

institute: Cancer Research UK

summary: Senescence is a stress responsive form of stable cell cycle exit. Senescent cells have a distinct gene expression profile, which is often accompanied by the spatial redistribution of heterochromatin into senescence-associated heterochromatic foci (SAHFs). Studying a key component of the nuclear lamina, lamin B1 (LMNB1), we report dynamic alterations in its genomic profile and their implications for SAHF formation and gene regulation during senescence. Genome-wide mapping reveals that LMNB1 is depleted during senescence, preferentially from the central regions of lamina-associated domains (LADs), which are enriched for H3K9me3. LMNB1 knockdown facilitates the spatial relocalization of perinuclear H3K9me3, thus promoting SAHF formation, which is inhibited by ectopic LMNB1 expression. Furthermore, despite the global reduction in LMNB1 protein levels, LMNB1 binding increases during senescence in a small subset of gene-rich regions where H3K27me3 also increases and gene expression becomes repressed. These results suggest that LMNB1 may contribute to senescence in at least two ways due to its uneven genomewide redistribution: firstly through the spatial re-organization of chromatin and, secondly, through gene repression.

overall_design: ChIP-seq for Lamin B1 in Growing and Ras Induced Senescence

first: Masashi

last: Narita


title: Genome-wide maps of chromatin state in C2C12 myoblast cells and myotubes.

status: Public on Aug 24 2013

city: Uppsala

last: Jiang

address: Husargatan 3, Box 582

department: Department Medical Biochemistry and Microbiology

country: Sweden

institute: Uppsala University

summary: We did ChIP-seq with anti- H3K4me3, H3K4me1, H3K4me2, H3K27me3, H3K27ac, and H3K36me3 antibodies in both C2C12 myoblasts and myotubes

overall_design: Examination of 6 different histone modifications in 2 cell types.

first: Tarjei

middle: S

last: Mikkelsen


title: RNA-Seq characterization of spinal cord injury transcriptome in acute/subacute phases: a resource for understanding the pathology at the systems level

city: Dallas

first: kenian

last: chen

address: 5323 Harry Hines Boulevard

department: Population and Data Science

institute: UTsouthwestern

summary:
Purpose: Spinal cord injury (SCI) is a devastating neurological disease without effective treatment. To generate a comprehensive view of the mechanisms involved in SCI pathology, we applied RNA-sequencing (RNA-seq) technology to characterize the temporal changes in global gene expression after contusive SCI in mice.

Method Part1: A total of 27 female C57BI/6J mice (10-16 weeks of age; 20-25g; The Jackson Laboratory, Bar Harbor, ME) were used with 9 mice in each of following groups: shame control, 2 and 7 days after SCI. The surgical procedure for SCI were described previously [PMID:23289019]. Briefly, after anesthetization with a mixed solution of ketamine (80 mg/kg, ip) and xylazine (10 mg/kg, ip), mice received a dorsal laminectomy at the 9th thoracic vertebral (T9) level to expose the spinal cord and then a moderate T9 contusive injury using an Infinite Horizons impactor (PrecisionSystems and Instrumentation) at 60 kdyn with the spinestabilized using steel stabilizers inserted under the transverse processes one vertebra above and below the injury [PMID:19196178] . The shame control mice received only a dorsal laminectomy without contusive injury. Afterwards, the wound was sutured in layers, bacitracin ointment(Qualitest Pharmaceuticals,Huntsville, AL) was applied tothe wound area, 0.1mL of a 20 mg/ml stock of gentamicin(ButlerSchein, Dublin, OH) was injected subcutaneously, and the animals recovered on a water-circulating heating pad. Then mice received analgesic agent, buprenorphin(0.05 mg/kg, SQ; Reckitt Benckise, Hull, England)twice a day for two days. Bladders were manually expressed until automatic voiding returned spontaneously, which generally was within 7 days. At 2 or 7 days after SCI, the mice were anesthetized again with ketamine and xylazine and perfused briefly with normal physical saline. The injured spinal cords were then dissected and three 0.5 mm pieces of spinal cord were cut in the injured epicenter. All spinal cords were immediately frozen in liquid nitrogen and processed for RNA isolation. The spinal cords from three mice were combined into one biological replicate for RNA extraction. Three biological replicates were used.

Method Part2: RNA-Seq was performed on the polyadenylated fraction of RNA isolated from tissue samples of acute (2D) and subacute phase (7D) and normal tissues (control, denoted as CTR hereafter). Three biological replicates were used for each phase.150-300 ng total RNAs were used for each sequencing library. RNA samples were polyA selected and paired-end sequencing libraries were constructed using TruSeq RNA Sample Prep Kit as described in the TruSeq RNA Sample Preparation V2 Guide (Illumina).The samples were then sequenced using the Illumina HiSeq sequencer. More than 30 million 100bp paired-end reads were generated from each biological replicate.

Method Part3: Read mapping and Transcriptome construction were done by using optimized pipeline which integrate Tophat followed by Cufflinks.

Result: We sequenced tissue samples from acute and subacute phases (2 days and 7 days after injury) and systematically characterized the transcriptomes with the goal of identifying pathways and genes critical in SCI pathology. The top enriched functional categories include ‘inflammation response’, ‘neurological disease’, ‘cell death and survival’ and ‘nervous system development’. The top enriched pathways include LXR/RXR Activation and Atherosclerosis Signaling etc. Furthermore, we developed a systems-based analysis framework in order to identify key determinants in the global gene networks of the acute and sub-acute phases. Some candidate genes that we identified have been shown to play important roles in SCI, which demonstrates the validity of our approach. There are also many genes whose functions in SCI have not been well studied and can be further investigated by future experiments. We have also incorporated pharmacogenomic information into our analyses. Among the genes identified, the ones with existing drug information can be readily tested in SCI animal models.

Conclusion: in this study we have described an example of how global gene profiling can be translated to screening genes of interest and generating new hypotheses. Additionally, the RNA-seq enables splicing isoform identification and the estimation of expression levels, thus providing useful information for increasing the specificity of drug design and reducing potential side effect. In summary, these results provide a valuable reference data resource for a better understanding of the SCI process in the acute and sub-acute phases.

overall_design: mRNA profiles of Acute/subacute phase Spinal Cord Injury sample from mice were generated by RNA-sequencing using Illumina HiSeq.

first: Kenian

first: Shuyun

last: Deng

first: Hezuo

last: lu

first: Jia

middle: Q

last: Wu

first: Qilin

last: Cao


title: Small RNA-seq and gene expression analysis reveal a miRNA profile of cancer-susceptibility in ATM deficient human mammary epithelial cells

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

type: Non-coding RNA profiling by genome tiling array


title: RNA-Seq analysis and targeted mutagenesis for improved free fatty acid production in an engineered cyanobacterium

city: Albuquerque

first: Anne

last: Ruffing

state: NM

department: Bioenergy and Defense Technologies

institute: Sandia National Laboratories

summary:
Background: High-energy-density biofuels are typically derived from the fatty acid biosynthesis pathway, thus establishing free fatty acids (FFAs) as important fuel precursors. FFA production using photosynthetic microorganisms like cyanobacteria allows for direct conversion of carbon dioxide into fuel precursors. Recent studies investigating cyanobacterial FFA production have demonstrated the potential of this process, yet FFA production was also shown to have negative physiological effects on the cyanobacterial host, ultimately limiting high yields of FFAs.
Results: Cyanobacterial FFA production was shown to generate reactive oxygen species (ROS) and lead to increased cell membrane permeability. To identify genetic targets that may mitigate these toxic effects, RNA-seq analysis was used to investigate the host response of Synechococcus elongatus PCC 7942. Stress response, nitrogen metabolism, photosynthesis, and protein folding genes were up-regulated during FFA production while genes involved in carbon and hydrogen metabolisms were down-regulated. Select genes were targeted for mutagenesis to confirm their role in mitigating FFA toxicity. Gene knockout of two porins and the overexpression of ROS-degrading proteins and hypothetical proteins reduced the toxic effects of FFA production, allowing for improved growth, physiology, and FFA production. Comparative transcriptomics, analyzing gene expression changes associated with FFA production and other stress conditions, identified additional key genes involved in cyanobacterial stress response.
Conclusions: A total of 15 gene targets were identified to reduce the toxic effects of FFA production. While single-gene targeted mutagenesis led to minor increases in FFA production, the combination of these targeted mutations may yield additional improvement, advancing the development of high-energy-density fuels derived from cyanobacteria.

sample_organism: Synechococcus elongatus PCC 7942 = FACHB-805

overall_design: Three strains (7942, SE01, and SE02) were analyzed at two time points (100 h and 240 h) with 3 biological replicates each (with the exception of SE02, 100 h having only 2 replicates due to RNA loss during sample preparation.)


title: H4K16 acetylation marks active genes and enhancers of embryonic stem cells, but does not alter chromatin compaction

type: Genome binding/occupancy profiling by genome tiling array


title: Targeted disruption of Hotair leads to homeotic transformation and de-repression of imprinted genes

status: Public on Aug 21 2013

city: Stanford

first: Kun

last: Qu

state: CA

address: 269 Campus Dr. CCSR 2150

department: Dermatology

institute: Stanford University


title: Targeted disruption of Hotair leads to homeotic transformation and de-repression of imprinted genes [RNA-Seq, ChIP-Seq]

summary: Long noncoding RNAs (lncRNAs) are thought to be prevalent regulators of gene expression, but the consequences of lncRNA inactivation in vivo are mostly unknown. Here we show that targeted deletion of mouse Hotair lncRNA leads to de-repression of hundreds of genes, resulting in homeotic transformation of the spine and malformation of metacarpal-carpal bones. RNA-seq and conditional inactivation reveal an ongoing requirement of Hotair to repress HoxD genes and multiple imprinted loci such as Dlk1-Meg3 and Igf2-H19. Hotair binds to both Polycomb repressive complex 2 that methylates histone H3 at lysine 27 (H3K27) and Lsd1 complex that demethylates histone H3 at lysine 4 (H3K4) in vivo. Hotair inactivation causes coordinate H3K27me3 loss and H3K4me3 gain at select target genes throughout the genome. These results reveal a shared regulatory mechanism to enforce silent chromatin state at Hox and imprinted genes via Hotair lncRNA.

overall_design: For RNA-seq data, we have 6 samples in total; 2 replica for the following three types: wildtype, heterozygous, and Hotair knock-out. For Chip-seq data, we have 6 samples in total; for each of the wildtype and Hotair knock-out samples, we have input, H3K4me3 and H3K27me3 histone marks.

first: Lingjie

last: Li

first: Bo

last: Liu

first: Orly

middle: L

last: Wapinski

first: Miao-Chih

last: Tsai

first: Jiajing

last: Zhang

first: Howard

middle: Y

last: Chang


title: Small RNA-seq and gene expression analysis reveal a miRNA profile of cancer-susceptibility in ATM deficient human mammary epithelial cells (Small RNA-Seq)

type: Non-coding RNA profiling by high throughput sequencing

summary: Deficiencies in the ATM gene are the underlying cause for ataxia telangiectasia, a congenital syndrome characterized by neurological, motor and immunological defects, as well as a predisposition to cancer risks. MicroRNAs (miRNAs) are small regulators of post-transcriptional gene expression and a useful tool for cancer diagnosis, staging, and prediction of therapeutic responses to clinical regimens. In particular, miRNAs have been used to develop signatures for breast cancer profiling.  We are interested in the consequences of ATM deficiency on miRNA expression in breast epithelial cells and the potential contribution to cancer predisposition. In this study we investigate the effects of ATM loss on the miRNA expression and related gene expression changes in normal human mammary epithelial cells (HME-CC). We have identified 81 significantly differently expressed miRNAs in the ATM-deficient HME-CCs using small RNA sequencing. Many of these differentially expressed miRNAs have been described and implicated in tumorigenesis and proliferation. These changes include down-regulation of tumor suppressor miRNAs, such as hsa-miR-29c and hsa-miR-16, as well as the over-expression of pro-oncogenic miRNAs hsa-miR-93 and hsa-mir-221. All 81 miRNAs were combined with genome wide gene expression profiles to investigate possible targets of miRNA regulation. We identified messenger RNA (mRNA) targets of these miRNAs that were also significantly regulated after the depletion of ATM. Predicted targets included many genes implicated in cancer formation and progression, including SOCS1 and the proto-oncogene MAF. Integrated analysis of miRNA and mRNA expression allows us to build a more complete understanding of the pathways and networks involved in the breast cancer predisposition observed in individuals deficient in ATM. This study highlights miRNA and predicted mRNA target expression changes in ATM-deficient HME-CCs and suggests a mechanism for the breast cancer-prone phenotype seen in ATM deficient cells and patients. Additionally, this study provides preliminary data for defining miRNA profiles that may be used prognostic biomarkers for breast cancer predisposition.

overall_design: Examination of small RNA population in human mammary epithelial cell lines. Each condition was preformed in triplicate.

first: Jill

middle: E

last: Hesse

first: Liwen

first: Cynthia

last: Innes

first: Richard

last: Paules


title: The cistrome of NKX3.1 in LNCaP prostate cancer cells

city: Nashville

first: Philip

middle: D

last: Anderson

state: TN

department: Pathology

institute: Vanderbilt University

summary: Here we report the genome-wide set of factors bound by NKX3.1 or control IgG in human prostate cancer cells (LNCaP).

overall_design: Examination of NKX3.1 binding in LNCaP prostate cancer cells

first: Sarki

last: Abdulkadir


first: Andrew

last: Clark

summary: The expression level in the parasitoid Nasonia vitripennis adult female samples was profiled and compared with the methylation pattern. Methylated and non-methylated genes showed markedly different patterns. The expression level was higher for methylated than non-methylated genes. non-nmethylated genes account for 99% of the genes that were not found to be expressed in the adult female RNA-seq data (FPKM < 0.1). Unlike methylated genes, the expression distribution of the non-methylated genes was bimodal with a lower expressed group and a moderately expressed group of genes, indicating that methylation status is not the only determinant of high expression in adult females. Methylated genes also have lower coefficient of variation (CV) of expression level across five developmental stages, suggesting that they are expressed more evenly across development.

overall_design: Profiling of expression level in adult female Nasonia vitripennis by RNA-seq

first: John

last: Werren

first: Xu

last: Wang


title: Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data

status: Public on Aug 20 2013

city: New York

first: Doron

last: Betel

state: NY

address: 1305 York Avenue (Box 140)

department: Medicine

institute: Weill Cornell Medical College

summary: A large number of computational methods have been recently developed for analyzing differential gene expression (DE) in RNA-seq data. We report on a comprehensive evaluation of the commonly used DE methods using the SEQC benchmark data set and data from ENCODE project. We evaluated a number of key features including: normalization, accuracy of DE detection and DE analysis when one condition has no detectable expression. We found significant differences among the methods. Furthermore, computational methods designed for DE detection from expression array data perform comparably to methods customized for RNA-seq. Most importantly, our results demonstrate that increasing the number of replicate samples significantly improves detection power over increased sequencing depth.

overall_design: The Sequencing Quality Control Consortium generated two datasets from two reference RNA samples in order to evaluate transcriptome profiling by next-generation sequencing technology. Each sample contains one of the reference RNA source and a set of synthetic RNAs from the External RNA Control Consortium (ERCC) at known concentrations. Group A contains 5 replicates of the Strategene Universal Human Reference RNA (UHRR), which is composed of total RNA from 10 human cell lines, with 2% by volume of ERCC mix 1. Group B includes 5 replicate samples of the Ambion Human Brain Reference RNA (HBRR) with 2% by volume of ERCC mix 2. The ERCC spike-in control is a mixture of 92 synthetic polyadenylated oligonucleotides of 250-2000 nucleotides long that are meant to resemble human transcripts.

first: Christopher

last: Mason

first: Paul

last: Zumbo

first: Franck

last: Rapaport

first: Raya

last: Khanin

first: Mono

last: Pirun

first: Azra

last: Krek

first: Nicholas

last: Socci

first: Yupu

last: Liang


title: Effects of Diet on Resource Utilization by a Model Human Gut Microbiota Containing Bacteroides cellulosilyticus WH2, a Symbiont with an Extensive Glycobiome (RNA-Seq)

city: Saint Louis

first: Nathan

last: McNulty

state: MO

address: 4444 Forest Park Ave. (5th Floor)

department: Center for Genome Sciences and Systems Biology

institute: Washington University School of Medicine

summary: The human gut microbiota is an important metabolic organ, yet little is known about how its individual species interact, establish dominant positions, and respond to changes in environmental factors such as diet. In this study, gnotobiotic mice were colonized with an artificial microbiota comprising 12 sequenced human gut bacterial species and fed oscillating diets of disparate composition. Rapid, reproducible, and reversible changes in the structure of this assemblage were observed. Time-series microbial RNA-Seq analyses revealed staggered functional responses to diet shifts throughout the assemblage that were heavily focused on carbohydrate and amino acid metabolism. High-resolution shotgun metaproteomics confirmed many of these responses at a protein level. One member, Bacteroides cellulosilyticus WH2, proved exceptionally fit regardless of diet. Its genome encoded more carbohydrate active enzymes than any previously sequenced member of the Bacteroidetes. Transcriptional profiling indicated that B. cellulosilyticus WH2 is an adaptive forager that tailors its versatile carbohydrate utilization strategy to available dietary polysaccharides, with a strong emphasis on plant-derived xylans abundant in dietary staples like cereal grains. Two highly expressed, diet-specific polysaccharide utilization loci (PULs) in B. cellulosilyticus WH2 were identified, one with characteristics of xylan utilization systems. Introduction of a B. cellulosilyticus WH2 library comprising >90,000 isogenic transposon mutants into gnotobiotic mice, along with the other artificial community members, confirmed that these loci represent critical diet-specific fitness determinants. Carbohydrates that trigger dramatic increases in expression of these two loci and many of the organism’s 111 other predicted PULs were identified by RNA-Seq during in vitro growth on 31 distinct carbohydrate substrates, allowing us to better interpret in vivo RNA-Seq and proteomics data. These results offer insight into how gut microbes adapt to dietary perturbations at both a community level and from the perspective of a well-adapted symbiont with exceptional saccharolytic capabilities, and illustrate the value of artificial communities.

sample_organism:
Bacteria
Bacteroides cellulosilyticus

platform_organism:
Bacteria
Bacteroides cellulosilyticus

overall_design: 116 samples total. In 26 of these samples, we evaluated community-wide gene expression using RNA isolated from the feces of a gnotobiotic mouse harboring an artificial community comprised of 12 human gut microbes. For these samples, we sought to determine the extent to which community gene expression is altered as a result of dietary oscillation. In the other 90 samples, we evaluated gene expression in a single species (B. cellulosilyticus WH2) grown in a defined medium supplemented with a single mono-, oligo-, or polysaccharide. For these samples, we sought to identify genes (particularly polysaccharide utilization loci) whose expression was significantly increased as a result of exposure to particular carbohydrates.


title: Exome sequencing of a panel of breast cancer cell lines to identify mutations

city: Portland

first: Laura

middle: M.

last: Heiser

state: OR

address: 3181 SW Sam Jackson Park Rd.

institute: OHSU

summary: This information was used to identify mutations associated with particular breast cancer subtypes, as well as associations with response to therapy.

overall_design: 75 breast cancer cell lines underwent exome sequencing to identify mutations.

first: Joe

middle: W

last: Gray


title: Modeling precision treatment of breast cancer

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

overall_design: Refer to individual Series


title: Interrogating translating RNAs and cell-type specific gene expression using Cre-activated translating ribosome affinity purification

city: Boston

first: Fei

last: Gu

state: MA

address: 320 Longwood Ave.

department: Cardiology

institute: Childrens hospital boston, Harvard Medical School

summary: We characterize a Cre-activated TRAP allele (Rosa26fsTRAP) to show that endothelium-specific activation of Rosa26fsTRAP identifies endothelial cell enriched transcripts, and that cardiomyocyte-restricted TRAP is a useful means to identify genes that are differentially expressed in cardiomyocytes in a disease model. We also show that TRAP is an effective means to study translational regulation, and we several nuclear-encoded mitochondrial genes are under strong translational control. These RNA-seq data show that the TRAP strategy and the Rosa26fsTRAP allele will be useful tools to probe cell type specific transcriptomes, and to study translational regulation.

overall_design: Study TRAP RNA and total RNA in two cases: heart specific tissues, Banding or Sham, using RNA-seq technology.

first: Pingzhu

last: Zhou

first: Yijing

last: Zhang

first: Qing

last: Ma

first: Daniel

last: Day

first: Aibin

last: He

first: Bin

first: Jing

last: Li

first: Sean

last: Stevens

last: Romo

first: Peter

last: Park

first: William

middle: T

last: Pu


title: H4K16 acetylation marks active genes and enhancers of embryonic stem cells, but does not alter chromatin compaction (II) [ChIP-Seq]

first: Gillian

last: Taylor

overall_design: ChIP-seq for H4K16 acetylation in undifferentiated 46c(sox1-gfp) ES cells, and FACS sorted day 5 Neural Progenitor Cells (differentiated with NB27 and Neuro2 medium supplements) , along with MNase digested input for both samples

first: Ragnhild

last: Eskeland

first: Betül

last: Hekimoglu-Balkan

first: Madapura

last: Pradeepa

first: Wendy

last: Bickmore


title: The SET-domain protein SUVR5 mediates H3K9me2 deposition and silencing at stimulus response genes in a DNA methylation independent manner

first: Hume

last: Stroud

address: 5323 Harry Hines Blvd

institute: UT Southwestern

first: Steve

last: Jacobsen


title: MiR-21 is targeted by STAT5 but dispensable for mammary gland development

city: Cheonan

first: Keunsoo

last: Kang

state: Chungnam

address: Dandae-ro 119

department: Microbiology

country: South Korea

institute: Dankook University

summary: In this study we identifies miR-21 to by under cytokine control through the transcription factor STAT5 and while miR-21 is differentially expressed during mammary gland development, miR-21 is dispensable for mammary development and lactation.

overall_design: We refer to wild-type mice (+/+) as WT and to mice lacking the mir-21 (-/-) as KO mice.

first: Yonatan

last: Feuermann

first: Lothar

last: Hennighausen


title: Effects of Diet on Resource Utilization by a Model Human Gut Microbiota Containing Bacteroides cellulosilyticus WH2, a Symbiont with an Extensive Glycobiome (COPRO-Seq)

first: Nathan

last: McNulty

overall_design: 611 samples total (221 from experiment 1, 390 from experiment 2). Evaluation of changes in an artificial gut community's structure over time as a result of dietary oscillation.


title: Effects of Diet on Resource Utilization by a Model Human Gut Microbiota Containing Bacteroides cellulosilyticus WH2, a Symbiont with an Extensive Glycobiome

sample_organism:
Bacteria
Bacteroides thetaiotaomicron VPI-5482
Bacteroides cellulosilyticus
Bacteroides sp. WH2
Blautia obeum ATCC 29174
Dorea longicatena DSM 13814
[Clostridium] scindens ATCC 35704
Bacteroides ovatus ATCC 8483
Bacteroides uniformis ATCC 8492
Bacteroides caccae ATCC 43185
Collinsella aerofaciens ATCC 25986
Thomasclavelia spiroformis DSM 1552
Phocaeicola vulgatus ATCC 8482
Parabacteroides distasonis ATCC 8503

platform_organism:
Bacteria
Bacteroides thetaiotaomicron VPI-5482
Bacteroides cellulosilyticus
Bacteroides sp. WH2
Blautia obeum ATCC 29174
[Ruminococcus] torques ATCC 27756
Dorea longicatena DSM 13814
[Clostridium] scindens ATCC 35704
Bacteroides ovatus ATCC 8483
Bacteroides uniformis ATCC 8492
Faecalibacterium prausnitzii M21/2
Bacteroides caccae ATCC 43185
Collinsella aerofaciens ATCC 25986
Thomasclavelia spiroformis DSM 1552
Phocaeicola vulgatus ATCC 8482
Parabacteroides distasonis ATCC 8503
Agathobacter rectalis ATCC 33656


title: RNA sequencing of stripe rust infected wheat leaves and isolated haustoria

status: Public on Aug 19 2013

city: Davis

first: Dario

last: Cantu

address: One Shields Ave

department: Plant Sciences

institute: UC Davis

summary: The fungus Puccinia striiformis f.sp. tritici (PST) is the causal pathogen of stripe rust in wheat. New highly virulent PST races appeared at the beginning of this century and spread rapidly causing significant yield losses in wheat production worldwide. Race PST-08/21 was isolated in the UK in 2008 Yr1, Yr2, Yr3, Yr4, Yr6, Yr9, Yr17, Yr27, Yr32, YrRob, YrSol. We applied the RNAseq approach to refine the gene prediction in de novo assembled PST 08/21 contigs and to determine which genes are expressed during wheat infections.

sample_organism: Puccinia striiformis f. sp. tritici 08/21

overall_design: Total RNA was extracted from a pool of stripe rust infected wheat leaves and from two biological replicates of haustoria isolates.

first: Diane

last: Saunders

first: Vanesa

last: Segovia

first: Jorge

last: Dubcovsky

first: Cristobal

last: Uauy


title: Transcriptome Analysis of Rice Root Heterosis by RNA-Seq

city: hangzhou

first: Rongrong

last: Zhai

address: No. 359, Tiyuchang Rd

institute: China National Rice Research Institute

summary: Heterosis is a phenomenon that hybrids exhibit superior performance relative to the parental phenotypes. However, most studies focused on aboveground agronomic traits. Thus, systematic investigation on root heterosis, particularly at reproductive stage in rice is needed to be carried out. The recent advent of RNA sequencing technology (RNA-Seq) provides an opportunity to conduct in-depth transcript profiling for heterosis study.Using the Illumina HiSeq 2000 platform, the root transcriptome of a super-hybrid rice Xieyou9308 and its parents were analyzed at tillering and heading stages. Totally, 829 and 4186 differentially expressed genes between the hybrid and its parents (DGHP) were detected at tillering stage and heading stage, respectively. In this study, the DGHP were significantly enriched in pathways such as carbohydrate metabolism and plant hormones signal transduction at heading stage, and most of the key genes involved in the two pathways were up-regulated in the hybrid. Several significant DGHP that could be mapped to QTLs for yield and root traits were also involved in carbohydrate metabolism and plant hormones signal transduction pathways. The candidate transcripts may underlie the heterosis and significantly contribute to root development and yield production.

overall_design: Root mRNA profiles of a super-hybrid rice Xieyou 9308 and its parents at tillering and heading stages were generated by deep sequencing, in duplicate, on Illumina Hiseq 2000 platform.

first: Rong-rong

first: Shi-hua

last: Cheng


title: Addiction of t(8;21) and inv(16) AML to native RUNX1 [ChIP-Seq data]

status: Public on Aug 18 2013

city: Rehovot

first: Yoram

last: Groner

address: 234 Herzl St.

department: Molecular Genetics

country: Israel

institute: Weizmann institute

summary: Cancer cells maintain a sensitive balance between growth-promoting oncogenes and apoptosis inhibitors. We show that WT RUNX1 is required for survival of t(8;21)-Kasumi-1 and inv(16)-ME-1 AML cell lines. The malignant AML phenotype is sustained by a delicate AML1-ETO/RUNX1 balance that involves competition for common DNA binding sites regulating a subset of AML1-ETO/RUNX1 targets.

overall_design: Genomewide sequencing data is included herein: Transcription factors RUNX1  c-terminus and n-terminus which is shared with AML1-ETO were profiled independently), AML1-ETO and AP4 were profiled using ChIP-Seq in Kasumi-1 cells, as well as control ChIP-Seq experiments of non immune serum. Two replicates were performed for each transcription factor profiling and control experiment.

first: Oren

last: Ben Ami

first: Dan

last: Friedman


title: Global DNA Methylation Remodeling Accompanies CD8 T Cell Effector Function

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

summary: In response to acute infection CD8 T cells differentiate into effector cells capable of clearing the antigen.  While the transcriptional and functional changes have previously been studied little is known of the epigenetic modifications that accompany this differentiation process.  To gain insights into CD8 T cell effector differentiation and the role of epigenetics, we mapped DNA methylation by MeDIP-seq in naive CD8 T cells and day 8 effector CD8 T cells that are induced following an acute infection.  We identified hundreds of thousands of differentially methylated regions (DMRs).  Promoter DNA methylation inversely correlated with gene expression and DMRs were enriched for functional transcription factor binding sites.  These data indicated that DNA methylation is dynamic during CD8 T cell differentiation and provide a map of possible regulatory regions important in this process.

overall_design: Examination of DNA methylation during CD8 T cell differentiation from naïve to day 8 effectors following acute infection

first: C

first: J

last: Boss


title: Distinct Global Shifts in Genomic Binding Profiles of Limb Malformation Associated HOXD13 Mutations

city: Berlin

first: Peter

last: Hansen

address: Augustenburger Platz 1

department: Institute for Medical Genetics and Human Genetics

country: Germany

institute: Charité-Universitätsmedizin Berlin

summary: We applied ChIP-seq to explore the effect of missense mutations in TFs on their genome wide binding profile. Using a retroviral expression system in chicken mesenchymal stem cells, we elucidated the mechanism underlying a novel missense mutation in HOXD13 (Q317K) associated with a complex hand and foot malformation phenotype. The glutamine at position 317 (position 50 of the homeodomain) is conserved in most homeodomains, a notable exception being bicoid-type homeodomains that have K at this position. Our results show that the mutation results in a shift in the binding profile of the mutant towards a bicoid/PITX1 motif. Gene expression analysis and functional assays using in vivo overexpression studies confirm that the mutation results in a partial conversion of HOXD13 into a TF with bicoid/PITX1 properties. A similar shift was not observed with the mutation Q317R, which is associated with brachysyndactyly, suggesting that the bicoid/PITX1-shift observed for Q317K might be related to the severe clinical phenotype.

overall_design: For each wt or mutant transcription factor two independent biological replicates were used for ChIP-seq together with corresponding input DNA as reference samples. For expression analysis one RNA sample for each wt and mutant transcription factor was used and compared to the expression level of cells infected with empty vector by RNA-seq.

first: Daniel

last: Ibrahim

first: Jochen

last: Hecht

first: Christian

last: Rödelsperger

first: Asita

last: Stiege

first: Sandra

last: Dölken

first: Denise

last: Horn

first: Marten

last: Jäger

first: Catrin

last: Janetzki

last: Krawitz

first: Gundula

last: Leschik

first: Florian

last: Wagner

first: Till

last: Scheuer

first: Mareen

last: Schmidt-von Kegler

first: Petra

last: Seemann

first: Bernd

last: Timmermann

middle: N

last: Robinson

first: Stefan

last: Mundlos


title: Genome-wide analysis of H4K5-acetylated genes in fear memory

city: Chicago

first: C. Sehwan

last: Park

state: IL

address: 375 East Chicago Ave

department: Pritzker School of Law

institute: Northwestern University

summary: Histone acetylation has been implicated in learning and memory in the brain, however, its function at the level of the genome and at individual genetic loci remains poorly investigated. This study examines a key acetylation mark, histone H4 lysine 5 acetylation (H4K5ac), genome-wide and its role in activity-dependent gene transcription in the adult mouse hippocampus following contextual fear conditioning. Using ChIP-Seq, we identified 23,235 genes in which H4K5ac correlates with absolute gene expression in the hippocampus. However, in the absence of transcription factor binding sites 150 bp upstream of the transcription start site, genes were associated with higher H4K5ac and expression levels. We further establish H4K5ac as a ubiquitous modification across the genome. Approximately one-third of all genes have above average H4K5ac, of which ~15% are specific to memory formation and ~65% are co-acetylated for H4K12. Although H4K5ac is prevalent across the genome, enrichment of H4K5ac at specific regions in the promoter and coding region are associated with different levels of gene expression. Additionally, unbiased peak calling for genes differentially acetylated for H4K5ac identified 114 unique genes specific to fear memory, over half of which have not previously been associated with memory processes. Our data provide novel insights into potential mechanisms of gene priming and bookmarking by histone acetylation following hippocampal memory activation. Specifically, we propose that hyperacetylation of H4K5 may prime genes for rapid expression following activity. More broadly, this study strengthens the importance of histone posttranslational modifications for the differential regulation of transcriptional programs in cognitive processes.

overall_design: 2 groups of 3 conditions: H4K5ac ChIP in contextual fear-conditioned (FC), IgG control of FC, input control of FC, H4K5ac ChIP in non-fear-conditioned control (CON), IgG control of CON, input control of CON

first: Sehwan

middle: C

first: Hubert

last: Rehrauer

first: Isabelle

last: Mansuy


title: Quantitative Different Analysis of antimicrobial peptide LL37 expressed in E.coli Top 10 under aerobic and anaerobic condition.

city: HANGZHOU

first: WEI

last: LIU

address: 198 SHIQIAO ROAD

institute: ZAAS

summary: We reported the transcriptional profiles of E.coli expressing antimicrobial peptide LL37 under stress response condition.

overall_design: 4 samples, two groups, one group is under aerobic condition, the other group is under anaerobic condition.  One of samples is E.coli which expressed LL37 as induction in each group, another sample is E.coli with no LL37 expression in vivo as control in each group.

first: Wei

last: Liu

first: Xin

last: Wang


title: MicroRNA sequencing and Novel HPV miRNA discovery in HPV cell lines and human tissue samples

city: Helsinki

first: Kui

last: Qian

address: Viikinkaari 4

country: Finland

institute: University of Helsinki

summary: Human papillomaviruses (HPV) preferentially infect keratinocytes of mucous membranes or skin and cause numerous benign and malignant lesions at different anatomical locations. A number of DNA viruses encode their own miRNAs as well. To date, no studies have been able to validate viral miRNAs in papillomavirus infected cells using standard sequencing or next generation sequencing techniques. We sequenced small RNA (sRNA) libraries of two HPV 16 immortalized cell lines, HPK IA and HPK II, and ten formalin fixed paraffin embedded (FFPE) tissue samples from HPV infected cervical epithelium by SOLiD 4 technology. We used the miRSeqNovel software, to predict novel miRNAs and their likely pre-miRNAs. We further validated (qRT-PCR, northern blotting and in situ hybridization) the candidate miRNAs in a number of tissue samples from HPV associated cervical disease and also in HPV 16 positive cell lines CaSki and SiHa. Altogether nine candidate microRNAs were identified. The expression of four out of five studied miRNAs was confirmed in human tissue or human epithelial cell lines harboring HPV 16.

overall_design: Small RNA (sRNA) libraries of two HPV 16 immortalized cell lines, HPK IA and HPK II, and ten formalin fixed paraffin embedded (FFPE) tissue samples from HPV infected cervical epithelium, were made according to SOLiD sequencing instructions.

first: Tuuli

last: Pietilä

first: Mikko

last: Rönty

first: Frederic

last: Michon

last: Frilander

first: Jarmo

last: Ritari

first: Jussi

last: Tarkkanen

first: Irma

last: Thesleff

first: Lars

last: Paulín

first: Petri

last: Auvinen

first: Eeva


title: The transcription factor IRF4 is essential for T cell receptor affinity mediated metabolic programming and clonal expansion of T cells [ChIP-seq]

status: Public on Aug 17 2013

city: Clayton

last: Shi

state: Victoria

address: Wellington Rd

country: Australia

institute: Monash University

summary: We demonstrate that transcription factor IRF4 is induced in a T cell receptor (TCR) affinity-dependent manner and functions as a dose-dependent regulator of the metabolic function of activated T cells. IRF4 regulates the expression of key molecules required for aerobic glycolysis of effector T cells, and is essential for clonal expansion and maintenance of effector function of antigen-specific CD8+ T cells.

overall_design: Examination of binding sites of transcription factor IRF4 in mouse CD8+ T cells.

first: Axel

last: Kallies

first: Kevin

last: Man

first: Annie

last: Xin

first: Stephen

last: Nutt

first: Gordon

middle: K

last: Smyth


title: Addiction of t(8;21) and inv(16) AML to native RUNX1

first: Yoram

last: Groner


title: Genome-wide effects of Spt6 on RNA pol II and Histone H3 occupancy in budding yeast (ChIP-Seq)

status: Public on Aug 16 2013

city: Aurora

first: David

middle: L.

last: Bentley

state: CO

department: Biochemistry and Mol. Genetics

institute: U. Colorado School of Medicine

summary: whole genome analysis of RNA pol II and histone H3 in WT and Spt6-depleted cells using a tetracycline regulated ts degron mutant, spt6-td.

overall_design: ChIP-seq of histone H3and pol II  in budding yeast (W303 background)

first: Hyunmin

last: Kim


title: Genome-wide effects of Spt6 on RNA pol II and Histone H3 occupancy in budding yeast


title: Chromatin position effects assayed by thousands of reporters integrated in parallel (cell lines with mPGK IRs)

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

summary: Reporter genes integrated into the genome are a powerful tool to reveal effects of regulatory elements and local chromatin context on gene expression. However, so far such reporter assays have been of low throughput. Here we describe a multiplexing approach for the parallel monitoring of transcriptional activity of thousands of randomly integrated reporters. More than 27,000 distinct reporter integrations in mouse embryonic stem cells, obtained with two different promoters, show ~1,000-fold variation in expression levels. Data analysis indicates that lamina-associated domains act as attenuators of transcription, likely by reducing access of transcription factors to binding sites. Furthermore, chromatin compaction is predictive of reporter activity. We also found evidence for cross-talk between neighboring genes, and estimate that enhancers can influence gene expression on average over ~20 kb. The multiplexed reporter assay is highly flexible in design and can be modified to query a wide range of aspects of gene regulation.

overall_design: TRIP assay of mPGK promotor; 11 clonal cell lines, 1 replicate each

first: Waseem

last: Akhtar

first: Johann

last: de Jong

first: Alexey

middle: V

last: Pindyurin

first: Ludo

last: Pagie

first: Wouter

last: Meuleman

first: Guillaume

middle: J

last: Filion

first: Jeroen

last: de Ridder

first: Anton

last: Berns

first: Lodewyk

middle: F

last: Wessels

first: Maarten

last: van Lohuizen


title: A Unifying Model for Molecular Determinants of the Pre-selection V Repertoire

city: La Jolla

first: Salvatore

last: Loguercio

state: California

address: 10550 North Torrey Pines Rd

department: MB

institute: TSRI

summary: Analysis of histone modifications in double negative thymocytes from RAG-/- mice

overall_design: For the ChIP-seq, input and immunoprecipitated DNA was given to The Scripps DNA Array Facility, where it was prepared for massively parallel sequencing on Illumina HiSeq 2000.


title: Chromatin position effects assayed by thousands of reporters integrated in parallel (RNA-Seq)

overall_design: mRNA profiles of 11 mouse embryonic cell lines each harboring multiple barcoded reporter constructs with mouse PGK promoter integrated at random positions in the genome, single replicate.


title: Chromatin position effects assayed by thousands of reporters integrated in parallel (mPGK TRIP pools)

overall_design: TRIP assay of mPGK promoter; 6 experiments, each with 2 technical replicates.


title: LncRNA-dependent mechanisms of androgen receptor-regulated gene activation programs

status: Public on Aug 15 2013

first: MICHAEL

middle: G

last: ROSENFELD

address: 9500 Gilman Drive

institute: HHMI/UCSD

overall_design: Refer to individual Series

first: Liuqing

last: Yang

first: Chunru

last: Lin

first: Bogdan

last: Tanasa

first: Wenbo

last: Li

first: Chunyu

last: Jin

first: Joy

first: Da

last: Meng

first: Kenneth

middle: A

last: Ohgi

first: Jie

last: Zhang

first: Christopher

middle: P

last: Evans

first: Michael

last: Rosenfeld


title: LncRNA-dependent mechanisms of androgen receptor-regulated gene activation programs [GRO-seq I]

summary: While thousands of long non-coding RNAs (lncRNAs) are expressed in higher eukaryotes, the potential regulatory roles of lncRNAs in regulated gene transcription programs remain rather poorly understood. Here, we report that two lncRNAs highly overexpressed in aggressive prostate cancer, PRNCR1 and PCGEM1, bind successively to the androgen receptor (AR) and strongly enhance both ligand-dependent and ligand-independent AR-mediated gene activation programs and proliferation in prostate cancer cells. Binding of PRNCR1 to the C-terminally acetylated AR on enhancers and its association with DOT1L appear to be required for recruitment of the second lncRNA, PCGEM, to the N-terminally methylated AR. Unexpectedly, recognition of the H3K4me3 promoter  mark by the PHD finger-domain of Pygopus2, recruited by PCGEM1, proves to enhance selective looping of AR-bound enhancers to target gene promoters in these cells, revealing a novel aspect of ligand-induced enhancer-promoter interactions. In “resistant” prostate cancer cells, these overexpressed lncRNAs can interact with, and are required for the robust activation of both truncated and full length AR, causing DHT-independent activation of the AR transcriptional program and cell proliferation. Conditionally-expressed short hairpin RNA (shRNA)-mediated targeting of these lncRNAs in these resistant cancer cell lines strongly suppressed xenograft growth in vivo. Together, these results suggest that these overexpressed lncRNAs can potentially serve as a required component of castration-resistance in prostatic tumors.

overall_design:
Global Run On (GRO) assay followed by high throughput sequencing (GRO-seq); after knocking down PYGO2
LNCaP cells were grown to 30-50% confluence and siRNA/ASO transfections were carried out using Lipofectamine 2000 (Invitrogen) according to the  manufacturer’s instructions. Control samples were transfected with scramble  ASO and control siRNA, respectively. On the following day of transfection,  the cells were cultured in UltraCULTURE (Phenol red free) + 5% Charcoal  Dextran Stripped (CDS) serum for 48 hours. For androgen induction, we treat  cells with DHT from a 100 uM stock in 70% ethanol to a final concentration of 100 nM for 1 hour
Control siRNA, -DHT
Control siRNA, +DHT
Pygo2 siRNA, -DHT
Pygo2 siRNA, +DHT


title: LncRNA-dependent mechanisms of androgen receptor-regulated gene activation programs [ChIRP-seq]

overall_design:
Global Run On (GRO) assay followed by high throughput sequencing (GRO-seq); ChIRP-seq data for a lincRNA (PCGEM1).
LNCaP cells were grown to 30-50% confluence and siRNA/ASO transfections were carried out using Lipofectamine 2000 (Invitrogen) according to the  manufacturer’s instructions. Control samples were transfected with scramble  ASO and control siRNA, respectively. On the following day of transfection,  the cells were cultured in UltraCULTURE (Phenol red free) + 5% Charcoal  Dextran Stripped (CDS) serum for 48 hours. For androgen induction, we treat  cells with DHT from a 100 uM stock in 70% ethanol to a final concentration of 100 nM for 1 hour
we have sequenced the DNA sequences that are associated with the presence of a RNA molecule on a genome wide scale.
PCGEM1 probe, -DHT
PCGEM1 probe, +DHT


title: Diverse patterns of genome-wide DNA targeting by transcriptional regulators in Drosophila melanogaster

first: Kevin

middle: P.

last: White

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

department: Institute for Genomics and Systems Biology

institute: University of Chicago

summary:
Understanding the regulatory genome remains a significant challenge.  Annotation of regulatory elements and identification of the transcription factors (TFs) targeting these elements are key steps in understanding how a given cell interprets its genetic blueprint. One goal of the modENCODE (model organism Encyclopedia of DNA Elements) project is to survey a diverse sampling of TFs, both DNA-binding and non-DNA binding factors, to provide a framework for the subsequent study of the mechanisms by which transcriptional regulators target the genome. Here we provide an updated map of the Drosophila melanogaster regulatory genome based on the location of 84 TFs at various stages of development. This regulatory map reveals a variety of genomic targeting patterns, including factors with strong preferences toward proximal promoter binding, factors that target intergenic and intronic DNA, and factors with distinct chromatin state preferences. The data also suggest the existence of a partially self-contained Polycomb regulatory network, and highlight the importance of Trithorax-like (Trl) in maintaining hotspots of DNA binding throughout development.  Furthermore, the data identify over 5,800 instances in which TFs target DNA regions with demonstrated enhancer activity. Regions of high TF co-occupancy are more likely to be associated with open enhancers used across cell types, while lower TF occupancy regions are associated with complex enhancers that are also regulated at the epigenetic level.  A putative regulatory network generated based on these 84 regulators reveals hundreds of co-binding events, thousands of potential regulatory interactions, and distinct regulatory strategies at developmental and housekeeping genes.  These data serve as a resource for the research community in the continued effort to dissect transcriptional regulatory mechanisms directing Drosophila development.
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: This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago.

first: Matthew

last: Slattery

first: Lijia

last: Ma

first: Rebecca

last: Spokony

first: Robert

last: Arthur

first: Pouya

last: Kheradpour

first: Anshul

last: Kundaje

first: Nicolas

last: Nègre

first: Alex

last: Crofts

first: Ryan

last: Ptashkin

first: Jennifer

last: Zieba

first: Alexander

last: Ostapenko

first: Sarah

last: Suchy

first: Alec

last: Victorsen

first: Nader

last: Jameel

first: A

last: Grundstad

first: Wenxuan

last: Gao

last: Moran

first: E

last: Rehm

middle: L

last: Grossman

first: Manolis

last: Kellis


title: LncRNA-dependent mechanisms of androgen receptor-regulated gene activation programs [GRO-seq II]

first: MICHAEL

last: ROSENFELD

overall_design:
Global Run On (GRO) assay followed by high throughput sequencing (GRO-seq); after knocking-down lincRNAs PCGEM1 and PRNCR1.
LNCaP cells were grown to 30-50% confluence and siRNA/ASO transfections were carried out using Lipofectamine 2000 (Invitrogen) according to the  manufacturer’s instructions. Control samples were transfected with scramble  ASO and control siRNA, respectively. On the following day of transfection,  the cells were cultured in UltraCULTURE (Phenol red free) + 5% Charcoal  Dextran Stripped (CDS) serum for 48 hours. For androgen induction, we treat  cells with DHT from a 100 uM stock in 70% ethanol to a final concentration of 100 nM for 1 hour
Scramble ASO, -DHT
Scramble ASO, +DHT
PRNCR1 ASO, -DHT
PRNCR1 ASO, +DHT
PCGEM1 ASO, -DHT
PCGEM1 ASO, +DHT

first: Liuqing

last: Yang

first: Chunru

last: Lin

first: Bogdan

last: Tanasa

first: Wenbo

last: Li

first: Chunyu

last: Jin

first: Joy

first: Da

last: Meng

first: Kenneth

last: Ohgi

first: Jie

last: Zhang

first: Christopher

last: Evans

first: Michael

last: Rosenfeld


title: Chromatin position effects assayed by thousands of reporters integrated in parallel

first: Bas

last: van Steensel

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


title: Genome-wide survey of YY1 targets in C2C12 cells by High-throughput sequencing

city: Shenzhen

first: Kun

last: Sun

address: Rm B505, No. 9 Duxue Road, Nanshan District

department: Cancer Research

institute: Shenzhen Bay Laboratory

summary: By applying ChIP-seq, we generated genome-wide maps of YY1 in skeletal myoblasts and myotubes. We found that YY1 binds to 1820 confident target with a large portion residing in the intergenic regions. In addition, YY1 was found to activate many loci, and there is no significant overlap between YY1 and Ezh2 targets, suggensting a Ezh2-independent manner. Further detailed study revealed that YY1 can regulate some lincRNAs which are fucntional in skeletal myogenesis. In this study, we identified a YY1-Yam-1-miR-715 (TF-lincRNA-miRNA) regulatory curcuit in myogensis.

overall_design: Examination of YY1 targets in myoblast versus myotubes

first: Huating

last: Wang

first: Hao

first: Leina

last: Lu

first: Xiaona

last: Chen

first: Lijun

first: Yu

last: Zhao

first: Liang

last: Zhou


title: Transcriptomics analysis of gene expression in normal and Smg6 deficient mouse ES cells

status: Public on Aug 14 2013

city: Beijing

first: Bao-Fa

address: Da-Tun Road

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

summary: RNA was isolated from control and Smg6 deficient ES cells using the TRIzol (Invitrogen) reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN (RNA integrity number) of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2000 (Illumina) in single-read mode, creating reads with a length of 50 bp. Sequencing chemistry v2 (Illumina) was used and samples were multiplexed in two samples per lane.

overall_design: Examination of gene expressive levels in normal and Smg6 deficient mouse ES cells

first: Zhao-Qi

first: Yun-Gui

last: Yang

first: Tangliang


title: Genome-wide comparative ChIP-seq data of H3K27me3 and RNA-seq data in Drosophila white prepupa on Illumina Genome Analyzer

first: Kevin

last: White

summary: This data consists of RNA-seq data of whole animal white pre pupa of four Drosophila species: Drosophila melanogaster, Drosophila simulans, Drosophila yakuba, and Drosophila pseudoobscura. The processed RPKM values are calculated following the method in Garber et al 2011 Nature Methods paper.

sample_organism:
Drosophila melanogaster
Drosophila pseudoobscura
Drosophila simulans
Drosophila yakuba

overall_design:
Examination of H3K27me3 in 4 Drosophila species and its correlation with gene expression levels in the same development stage
relevant ChIP-seq data can be found in GSE27111 [for melanogaster], GSE23537 SuperSeries [for simulans, yakuba, and pseudoobscura] (SubSeries: GSE25663, GSE25668, GSE50819)

first: R

last: Arthur

first: K


title: Genome-wide identification of binding sites for NAC and YABBY transcription factors and co-regulated genes during soybean seedling development by ChIP-Seq and RNA-Seq.

city: Urbana

first: Lila

middle: O.

last: Vodkin

address: 1201 W. Gregory Dr.

department: Crop Sciences

institute: University of Illinois

summary: In order to dissect the gene regulatory network during the functional transition of cotyledons from non-photosynthetic storage tissue to metabolically active photosynthetic tissue, we constructed ChIP-Seq libraries for NAC and YABBY transcription factors using pooled cotyledons from seedling developmental stage 4 and stage 5.  Millions of raw reads obtained from ChIP-Seq libraries were aligned to the reference soybean genome using the ultrafast Bowtie aligner to obtain quantitative data for genome matched reads. MACS software was used to call peaks representing enriched binding sites for NAC and YABBY transcription factors. Based on our ChIP-Seq data, we identified 72 genes are potentially regulated by NAC transcription factor and 96 genes by YABBY transcription factor. The motif analysis using MEME discovered three separate motifs for the NAC and YABBY transcription factors. For the NAC transcription factor, three commonly found motifs were G[AT]G[AG]G[AG]GA, C[AC]C[GA][TC][GA]CC and TGGGCC . The first one matched to a known zinc finger motif and the last two were identified as leucine zippers in the database of plant transcription factor binding motifs, JASPAR CORE plants. Similarly the three most commonly found motifs for YABBY transcription factors are CC [CA][TC]C[TA][CT]C, GA[AG]AGAAA and CCCCAC . The first two motifs matched to a known zinc finger motif and the last one was an AP2 MBD-like motif.

overall_design: Construction of ChIP-Seq libraries for NAC and YABBY transcription factors using germinating cotyledons from seedling developmental stages

first: Md

last: Shamimuzzaman

middle: O


title: Program specificity for Ptf1a in Pancreas versus Neural Tube Development correlates with distinct collaborating cofactors and chromatin accessibility

city: Dallas

first: Jane

middle: E

last: Johnson

address: 5323 Harry Hines Blvd

department: Neuroscience

institute: UT Southwestern Medical Center

summary: Ptf1a is a lineage-specific basic-helix-loop-helix transcription factor critical in the development of both the pancreas and nervous system. How one transcription factor controls diverse programs of gene expression is a fundamental question in developmental biology. To uncover molecular strategies for the program-specific functions of Ptf1a, we identified bound genomic regions in vivo during development of both tissues. A majority of regions bound by Ptf1a are tissue-specific, lie near genes needed for proper formation and maturation of each tissue, and reflect regions of open chromatin.  Information for the specificity of Ptf1a binding and function is encoded in the DNA surrounding the Ptf1a-bound sites, since Ptf1a-bound regions are sufficient to direct tissue-restricted reporter expression when tested in transgenic mice. Fox and Sox factors were identified as lineage specific modifiers of Ptf1a binding, since binding motifs for these factors are enriched in Ptf1a-bound regions in pancreas and neural tube, respectively. Although Ptf1a and Foxa2 co-localize to sites in embryonic pancreas and can act synergistically in cell transfection assays, biochemical experiments detected no physical interaction between the two factors. These findings indicate that lineage-specific chromatin landscapes likely constrain the functions of Ptf1a, and identify Fox and Sox gene families as part of this process.

overall_design:
RNA-Seq: Examination of gene expression in Ptf1a expressing cells (NT E.12.5, Pancreas E15.5)
ChIP-Seq: Examination of chromatin occupancy in 2 tissue types (E12.5 NT and 17.5 Pancreas).
Faire-Seq: Examination of open chromatin in 2 tissue types (E12.5 NT and 17.5 Pancreas).

first: David

middle: M

last: Meredith

first: Mark

middle: D

last: Borromeo

first: Tye

last: Deering

first: Bradford

last: Casey

first: Trisha

last: Savage

first: Paul

middle: R

last: Mayer

first: Chinh

last: Hoang

first: Kuang-Chi

last: Tung

first: Manonmani

last: Kumar

first: Chengcheng

last: Shen

first: Galvin

middle: H

last: Swift

first: Raymond

last: MacDonald


title: The BTB-zinc finger transcription factor Abrupt acts as an epithelial oncogene in Drosophila through maintaining a progenitor-like cell state

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: Center for Genomic Regulation (CRG)

summary: The capacity of tumor cells to maintain continual overgrowth potential has been linked to the commandeering of normal self-renewal pathways. Using an epithelial cancer model in Drosophila we carried out an overexpression screen for oncogenes capable of cooperating with the loss of the epithelial apico-basal cell polarity regulator, scribbled, and identified the cell fate regulator, Abrupt, a BTB-zinc finger protein.  Abrupt overexpression alone is insufficient to transform cells, but in cooperation with scrib loss of function, Abrupt promotes the formation of massive tumors in the eye/antennal disc. The steroid hormone receptor coactivator, Taiman (SRC3/AIB1), is known to associate with Abrupt, and Taiman overexpression also drives tumor formation in cooperation with the loss of Scribbled. Expression arrays and ChIP-Seq indicates that Abrupt overexpression represses a large number of genes, including steroid hormone-response genes and multiple cell fate regulators, thereby maintaining cells within an epithelial progenitor-like state. The progenitor-like state is characterised by the failure to express the conserved Eyes absent/Dachshund regulatory complex in the eye disc, and in the antennal disc by the failure to express cell fate regulators that define the temporal elaboration of the appendage along the proximo-distal axis downstream of Distalless. Loss of scribbled promotes cooperation with Abrupt through impaired Hippo signaling, which is required and sufficient for cooperative overgrowth with Abrupt, and JNK signaling, which is required for tumor cell migration/invasion but not overgrowth. These results thus identify a novel cooperating oncogene, mammalian family members of which are also known oncogenes, and demonstrate that epithelial tumors in Drosophila can be characterised by the maintenance of a progenitor-like state.

overall_design: ChIP-Seq of Abrupt, ChIP-Seq of Abrupt (scrib-), Input, Input (scrib-)

first: Nezaket

last: Turkel

first: Virender

last: Sahota

first: Jessica

last: Bolden

first: Karen

last: Goulding

last: Doggett

last: Martin-Blanco

first: Montserrat

last: Corominas

first: Toshiro

last: Aigaki

first: Helena

last: Richardson

first: Anthony

last: Brumby


title: A Unifying Model for Molecular Determinants of the Pre-selection Vb Repertoire [RNA-Seq]

first: Eugene

last: Oltz

address: 660 S Euclid Avenue

department: Pathology and Immunology

institute: Washington Univeristy in St.Louis

summary: The primary antigen receptor repertoire is sculpted by the process of V(D)J recombination, which must strike a balance between diversification and favoring gene segments with specialized functions. The precise determinants of how often gene segments are chosen to complete variable region coding exons remain elusive. We have quantified Vβ usage in the pre-selection Tcrb repertoire and report relative contributions of 14 distinct features in shaping their recombination efficiencies, including transcription, chromatin environment, spatial proximity to their DβJβ targets, and quality of recombinase recognition elements. Computational analyses provide a unifying model, revealing a minimal set of eight parameters that are predictive of Vβusage, dominated by chromatin modifications associated with transcription, but largely independent of the precise spatial proximity to DβJβclusters.

overall_design: Transcription profiles of mouse DN thymocytes from Rag1 KO mice were generated by deep sequencing, using Illumina Hi-Seq 2000.

first: S

last: Gopalakrishnan

first: Alexander

last: Predeus

first: Maxim

last: Artyomov


title: A Unifying Model for Molecular Determinants of the Pre-selection Vb Repertoire


title: Transcription factor binding in human cells occurs in dense clusters formed around cohesin anchor sites

city: Stockholm

first: Martin

last: Enge

address: CCK, Z4

department: Dep of Oncology-Pathology

institute: Karolinska Institute

summary: During cell division, transcription factors (TFs) are removed from chromatin twice, during DNA synthesis, and during condensation of chromosomes. How TFs can efficiently find their sites following these stages has been unclear. Here, we have analyzed the binding pattern of expressed TFs in human colorectal cancer cells. We find that binding of TFs is highly clustered, and that the clusters are enriched in binding motifs for several major TF classes. Strikingly, almost all clusters are formed around cohesin, and loss of cohesin decreases both DNA accessibility and binding of TFs to clusters. We show that cohesin remains bound in S phase, holding the nascent sister chromatids together at the TF cluster sites. Furthermore, cohesin remains bound to the cluster sites when TFs are evicted in early M-phase. These results suggest that cohesin binding functions as a cellular memory that promotes re- stablishment of TF clusters after DNA replication and chromatin condensation.

overall_design: Examination of TF binding by ChIP-seq in LoVo CRC cell-lines.

first: Jian

last: Yan


title: Maternal overnutrition causes insulin resistance and alters skeletal muscle oxidative phosphorylation in adult rat offspring

status: Public on Aug 13 2013

city: Melbourne

first: Mark

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

institute: Burnet Institute

summary: Maternal obesity can program metabolic syndrome in offspring but the mechanisms are not well characterized. Moreover, the consequences of maternal overnutrition in the absence of frank obesity remain poorly understood. This study aimed to determine the effects of maternal consumption of a high fat-sucrose diet on the skeletal muscle metabolic and transcriptional profiles of adult offspring. Female Sprague Dawley rats were fed either a diet rich in saturated fat and sucrose (HFD, 23.5% fat, 20% sucrose wt/wt) or a standard chow diet (NFD, 7% fat, 10% sucrose w/w) for the 3 weeks prior to mating and throughout pregnancy and lactation. Although maternal weights were not different between groups at conception or weaning, HFD dams were ~22% heavier than chow fed dams from mid-pregnancy until 4 days post-partum. Adult male offspring of HFD dams were not heavier than controls but demonstrated features of insulin resistance including elevated plasma insulin concentration (+40%, P<0.05). Next Generation mRNA Sequencing was used to identify differentially expressed genes in the soleus muscle of offspring, and Gene Set Enrichment Analysis (GSEA) to detect coordinated changes that are characteristic of a biological function. GSEA identified 15 pathways enriched for up-regulated genes, including cytokine signaling (P<0.005), starch and sucrose metabolism (P<0.017), and inflammatory response (P<0.024). A further 8 pathways were significantly enriched for down-regulated genes including oxidative phosphorylation (P<0.004) and electron transport (P<0.022). Western blots confirmed a ~60% reduction in the phosphorylation of the insulin signaling protein Akt (P<0.05) and ~70% reduction in mitochondrial complexes II (P<0.05) and V expression (P<0.05). On a normal diet, offspring of HFD dams developed an insulin resistant phenotype, with transcriptional evidence of muscle cytokine activation, inflammation and mitochondrial dysfunction. These data indicate that maternal overnutrition, even in the absence of pre-pregnancy obesity can promote metabolic dysregulation and predispose offspring to type 2 diabetes.

overall_design: Messenger RNA profile of skeletal muscle of male offspring from female Sprague Dawley rats fed either a diet rich in saturated fat and sucrose (HFD, 23.5% fat, 20% sucrose wt/wt) or a standard chow diet (NFD, 7% fat, 10% sucrose w/w) for the 3 weeks prior to mating and throughout pregnancy and lactation. There were 5 HFD samples compared to 6 NFD control samples.

first: Celine

last: Latouche

first: Sarah

last: Heywood

last: Henry

first: Ross

last: Lazarus

first: Assam

last: El-Osta

first: James

last: Armitage

first: Bronwyn

last: Kingwell


title: Chromatin position effects assayed by thousands of reporters integrated in parallel (tet-Off TRIP pools)

first: Bas

last: van Steensel

overall_design: TRIP assay of tet-Off promotor; 4 experiments, each with 2 technical replicates. Each experiment was induced at 4 different concentrations of doxycycline.

first: Waseem

last: Akhtar

first: Johann

last: de Jong

first: Alexey

last: Pindyurin

first: Ludo

last: Pagie

first: Wouter

last: Meuleman

first: Guillaume

last: Filion

first: Jeroen

last: de Ridder

first: Anton

last: Berns

first: Lodewyk

last: Wessels

first: Maarten

last: van Lohuizen


title: Cohesin-based chromatin interactions enable regulated gene expression within pre-existing architectural compartments.

first: Andre

last: Faure

department: EMBL-CRG Systems Biology Unit

institute: Centre for Genomic Regulation (CRG)

summary: Chromosome conformation capture approaches have shown that interphase chromatin is organized into an architectural framework of Mb-sized compartments and sub-Mb-sized topological domains. Cohesin controls chromosome topology to facilitate DNA repair and chromosome segregation in cycling cells, and also associates with active enhancers and promoters and with CTCF to form long-range interactions important for gene regulation. We find that architectural compartments - a major feature of interphase chromatin organization – are maintained in non-cycling mouse thymocytes after genetic depletion of cohesin in vivo. Cohesin was however required for specific long-range interactions within permissive (A-type) compartments, where cohesin-regulated genes reside. Cohesin depletion diminished interactions between cohesin-bound sites, while alternative interactions between chromatin features associated with transcriptional activation and repression became more prominent, with corresponding changes in gene expression. Our findings indicate that cohesin-mediated long-range interactions facilitate discrete gene expression states within pre-existing chromosomal compartments.

overall_design: The chromatin binding of cohesin, the cohesin-loading loading complex and Mediator was analysed by ChIP-sequencing in thymocytes for the respective subunits Rad21, NIPBL and Med1. The role of the cohesin complex in transcriptional regulation was investigated using RNA-sequencing in wild type and Rad21 KO thymocytes, while the global role of cohesin in chromatin organisation was investigated by Hi-C in wild type and Rad21 KO thymocytes. This approach allowed us to integrate the binding of cohesin and its associated factors with changes in transcription and chromatin organisation upon cohesin depletion.

first: Matthias

last: Merkenschlager

first: Job

last: Dekker


title: ChIP-seq analysis of M1BP in Drosophila S2R+ cells

city: University Park

first: David

middle: Scott

last: Gilmour

state: Pennsylvania

address: 465 North Frear

department: Biochemistry and Molecular Biology

institute: Penn State University

summary: The genomic distribution of a novel transcription factor called M1BP was determined in Drosophila S2R+ cells

overall_design: Polyclonal antibody raised against M1BP was used to immunoprecipitate M1BP-DNA adducts generated by treating Drosophila cells with formaldehyde, lysing the cells, and shearing DNA by sonication.  Immunoprecipitated DNA was sequenced using the AB SOLiD system.

first: Jian

last: Li

middle: S


title: The newly identified transcription factor M1BP ad GAGA factor orchestrate distinct mechanisms of transcriptional regulation on paused genes

overall_design: Refer to individual Series


title: Intragenic DNA methylation modulates alternative splicing by recruiting MeCP2 to promote exon recognition [RNA-Seq]

city: Cincinnati

first: Iouri

last: Chepelev

state: OH

address: 3200 Vine St

institute: US Department of Veterans Affairs Medical Center

summary: Although the function of DNA methylation in gene promoter regions is well established in transcriptional repression, the function of the evolutionarily conserved widespread distribution of DNA methylation in gene body regions remains incompletely understood. Here, we show that DNA methylation is enriched in included alternatively spliced exons (ASEs) and inhibiting DNA methylation results in aberrant splicing of ASEs. The methyl-CpG binding protein MeCP2 is enriched in included ASEs, particularly those that are also highly DNA methylated, and inhibition of DNA methylation disrupts specific targeting of MeCP2 to exons. Interestingly, ablation of MeCP2 results in increased nucleosome acetylation and aberrant skipping events of ASEs. We further show that inhibition of histone deacetylases leads to a highly significant overlap of exon skipping events caused by knocking-down MeCP2. Together, our data indicate that intragenic DNA methylation operates in exon definition to modulate alternative splicing and can enhance exon recognition via recruitment of the multifunctional protein MeCP2, which thereby maintains local histone hypoacetylation through its established interaction with HDACs.

overall_design: RNA-Seq in IMR90 and HCT116

first: Alika

middle: K

last: Maunakea

first: Kairong

last: Cui

first: Keji

last: Zhao


title: Epigenetic determinants of muscle stem cell quiescence and chronological aging (ChIP-seq)

city: Palo Alto

first: Ling

last: Liu

address: 300 Pasteur Drive

institute: Stanford University

summary: Skeletal muscle is a post-mitotic tissue that exhibits an extremely low turnover in the absence of disease or injury. At the same time, muscle possesses remarkable regenerative capacity mediated by satellite cells (SCs) that reside in close association with individual myofibers, underneath the fiber’s basal lamina. Consistent with the low turnover of the muscle, SCs in adult animals are mitotically quiescent and therefore provide an excellent model to study stem cell quiescence. As an organism grows older, the resident stem cells are exposed to a deteriorating environment and experience chronological aging. In stem cells with high turnover, the effects of chronological aging are superimposed upon the effects of the replicative aging that results from DNA replication and cell division. On the contrary, SCs experience minimal replicative aging due to their low turnover. They are thus a good model to study the consequence of chronological aging of quiescent stem cells. We have developed an isolation protocol to selectively enrich SCs by FACS from adult mice and applied the ChIP-seq technology to obtain H3K4me3, H3K27me3 and H3K36me3 from quiescent and activated SCs from young mice and from quiescent SCs from old mice. Our analysis aims to understand the chromatin features underlying stem cell properties such as quiecence and lineage-potency, and to understand how the chromatin structure of a quiescent stem cell pouplation changes with age.

overall_design: VCAM+/CD31-/CD45-/Sca1- quiescent satellite cells (QSCs) were isolated by FACS from hindlimb muscle of uninjured 2-3- or 22-24-month old mice and processed for ChIP-seq.

first: Thomas

last: Rando


title: Transcriptional profiling of a breast cancer cell line panel using RNAseq technology

city: Portland

first: Laura

middle: M.

last: Heiser

address: 3181 SW Sam Jackson Park Rd.

institute: OHSU

summary: 56 breast cancer cell lines were profiled to identify patterns of gene expression associated with subtype and response to therapeutic compounds.

overall_design: Cell lines were profiled in their baseline, unperturbed state.

first: Joe

middle: W

last: Gray


title: TCF_WPP_ChIP-seq

status: Public on Aug 11 2013

city: Toronto

first: DCC

last: modENCODE

state: Ontario

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

institute: Ontario Institute for Cancer Research

summary:
modENCODE_submission_5025
This submission comes from a modENCODE project of Kevin White. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The White Lab is aiming to map the association of all the Transcription Factors (TF) on the genome of Drosophila melanogaster. One technique that we use for this purpose is chromatin immunoprecipitation coupled with deep sequencing (ChIP-seq) utilizing an Illumina next generation sequencing platform. The data generated by ChIP-seq experiments consist basically of a plot of signal intensity across the genome. The highest signals correspond to positions in the genome occupied by the tested TF.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: Y cn bw sp; Developmental Stage: White Prepupae (WPP); Genotype: y[1] oc[R3.2]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] lab[R4.2] MstProx[1] GstD5[1] Rh6[1];  EXPERIMENTAL FACTORS: Developmental Stage White Prepupae (WPP); Strain Y cn bw sp; Antibody tgo mouse Crews (target is tango)

first: Kevin

last: White

first: Lijia

last: Ma

first: Matthew

last: Slattery


title: Cooler temperatures destabilize RNA interference and increase susceptibility of disease vector mosquitoes to viral infection

city: Blacksburg

last: Myles

state: VA

address: Fralin Biotechnology Center

department: Fralin Life Science Institute

institute: Virginia Tech

summary: The impact of global climate change on the transmission dynamics of infectious diseases is the subject of extensive debate. The transmission of mosquito-borne viral diseases is particularly complex, with climatic variables directly affecting many parameters associated with the prevalence of disease vectors. While evidence shows that warmer temperatures often decrease the extrinsic incubation period of an arthropod-borne virus (arbovirus), exposure to cooler temperatures often predisposes disease vector mosquitoes to higher infection rates. RNA interference pathways are essential to antiviral immunity in the mosquito; however, few experiments have explored the effects of temperature on the RNAi machinery.

sample_organism:
Aedes aegypti
Aedes albopictus

platform_organism:
Aedes aegypti
Aedes albopictus

overall_design: Total small RNAs (miRNAs, siRNAs, piRNAs, etc.) were isolated and sequenced from the heads of sensor strain Aedes aegypti mosquitoes, or from the whole bodies of CHIKV-infected Aedes albopictus mosquitoes 8 hours post infection. Mosquitoes were grown at 18C or 28C in replicates of 1 (Ae. aegypti) or 3 (Ae. albopictus).

first: Zach

middle: N

last: Adelman

first: Michelle

last: Anderson

first: Michael

last: Wiley

first: Marta

last: Murreddu

first: Hazitha

last: Samuel

first: Elaine

last: Morazzani


title: TCF_nonISO1_0-8_embryonic_ChIP-seq

summary:
modENCODE_submission_5023
This submission comes from a modENCODE project of Kevin White. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The White Lab is aiming to map the association of all the Transcription Factors (TF) on the genome of Drosophila melanogaster. One technique that we use for this purpose is chromatin immunoprecipitation coupled with deep sequencing (ChIP-seq) utilizing an Illumina next generation sequencing platform. The data generated by ChIP-seq experiments consist basically of a plot of signal intensity across the genome. The highest signals correspond to positions in the genome occupied by the tested TF.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: Hr46-GFP; Developmental Stage: Embryo 0-8; Genotype: PBac{y[+]-attP-3B}VK00033; Sex: Unknown; Transgene: Hr46 genomic coding region;  EXPERIMENTAL FACTORS: Developmental Stage Embryo 0-8; Strain Hr46-GFP; Antibody tgo mouse Crews (target is tango)


title: TCF_W3L_ChIP-seq

summary:
modENCODE_submission_5024
This submission comes from a modENCODE project of Kevin White. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The White Lab is aiming to map the association of all the Transcription Factors (TF) on the genome of Drosophila melanogaster. One technique that we use for this purpose is chromatin immunoprecipitation coupled with deep sequencing (ChIP-seq) utilizing an Illumina next generation sequencing platform. The data generated by ChIP-seq experiments consist basically of a plot of signal intensity across the genome. The highest signals correspond to positions in the genome occupied by the tested TF.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: Y cn bw sp; Developmental Stage: L3; Genotype: y[1] oc[R3.2]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] lab[R4.2] MstProx[1] GstD5[1] Rh6[1]; Sex: Unknown;  EXPERIMENTAL FACTORS: Developmental Stage L3; Strain Y cn bw sp; Antibody tgo mouse Crews (target is tango)


title: dTBP_0-8h_embryonic_ChIP-seq

summary:
modENCODE_submission_5022
This submission comes from a modENCODE project of Kevin White. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The White Lab is aiming to map the association of all the Transcription Factors (TF) on the genome of Drosophila melanogaster. One technique that we use for this purpose is chromatin immunoprecipitation coupled with deep sequencing (ChIP-seq) utilizing an Illumina next generation sequencing platform. The data generated by ChIP-seq experiments consist basically of a plot of signal intensity across the genome. The highest signals correspond to positions in the genome occupied by the tested TF.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: Exd-GFP-13T; Developmental Stage: Embryo 0-8; Genotype: w; PBac{y[+]-attP-3B}VK00033; Sex: Unknown; Transgene: exd genomic coding region with stop codon replaced with GFP;  EXPERIMENTAL FACTORS: Developmental Stage Embryo 0-8; Strain Exd-GFP-13T; Antibody Tbp (target is Tbp)


title: FOXO3 shares common targets with ASCL1 genome-wide and inhibits ASCL1-dependent neurogenesis

city: Stanford

first: Anne

last: Brunet

address: 300 Pasteur Drive,

department: Genetics

summary: FOXO transcription factors are central regulators of longevity from worms to humans. FOXO3 – the FOXO isoform associated with exceptional human longevity – preserves adult neural stem cell pools. Here we identify FOXO3 direct targets genome-wide in primary cultures of adult neural progenitor cells (NPCs). Interestingly, FOXO3-bound sites are enriched for motifs for bHLH transcription factors and FOXO3 shares common targets with the pro-neuronal bHLH transcription factor ASCL1/MASH1 in NPCs. Analysis of the chromatin landscape reveals that FOXO3 and ASCL1 are particularly enriched at the enhancers of genes involved in neurogenic pathways. Intriguingly, FOXO3 inhibits ASCL1-dependent neurogenesis in NPCs and direct neuronal conversion in fibroblasts. FOXO3 also restrains neurogenesis in vivo. Our study identifies a genome-wide interaction between the pro-longevity transcription factor FOXO3 and the cell fate determinant ASCL1, and raises the possibility that FOXO3’s ability to restrain ASCL1-dependent neurogenesis may help preserve the neural stem cell pool.

overall_design: ChIP-seq profiles of two transcription factors (FOXO3 and ASCL1) and three histone marks (H3K4me1, H3K4me3 and H3K27me3) in adult mouse neural progenitor cells.


title: Su(H)_0-8_embryonic_ChIP-seq

summary:
modENCODE_submission_5017
This submission comes from a modENCODE project of Kevin White. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The White Lab is aiming to map the association of all the Transcription Factors (TF) on the genome of Drosophila melanogaster. One technique that we use for this purpose is chromatin immunoprecipitation coupled with deep sequencing (ChIP-seq) utilizing an Illumina next generation sequencing platform. The data generated by ChIP-seq experiments consist basically of a plot of signal intensity across the genome. The highest signals correspond to positions in the genome occupied by the tested TF.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: Y cn bw sp; Developmental Stage: Embryo 0-8; Genotype: y[1] oc[R3.2]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] lab[R4.2] MstProx[1] GstD5[1] Rh6[1]; Sex: Unknown;  EXPERIMENTAL FACTORS: Developmental Stage Embryo 0-8; Strain Y cn bw sp; Antibody Su(H) (target is fly genes:Su(H))