title: seq-ab8896_H3K9me1_104560_N2_L3

first: DCC

last: modENCODE

summary:
modENCODE_submission_5036
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: L3 Larva; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  EXPERIMENTAL FACTORS: Developmental Stage L3 Larva; temp (temperature) 20 degree celsius; Strain N2; Antibody ab8896 H3K9me1:104560 (target is H3K9me1)


title: seq-Ab2621_H3K79me3_FEM2_AD

status: Public on Jul 26 2013

city: Toronto

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_5173
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: 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 AB2621 H3K79me3:361576 (target is H3K79me3)

first: Abby

last: Dernburg

first: Christina

last: Whittle


title: Comparative expression profiling of miRNA during anther development in genetic male sterile and wild type cotton [small RNA]

status: Public on Jul 28 2013

city: Anyang

first: Ming ming

last: Wei

address: Huang he road 38

country: China

institute: Cotton Research Institute, Chinese Academy of Agriculture Sciences (CAAS)

type: Non-coding RNA profiling by high throughput sequencing

summary: Genetic male sterility (GMS) in cotton (Gossypium hirsutum) plays an important role in the utilization of hybrid vigor. However, the molecular mechanism of the GMS is still unclear. While numerous studies have demonstrated that microRNAs (miRNA) regulate flower and anther development, whether different small RNA regulations exist in GMS and its wild type is unclear. To investigate the global expression and complexity of small RNAs during cotton anther development, three small RNA libraries were constructed from the anthers of three development stages each from fertile wild type (WT) and its GMS mutant cotton.

overall_design: Examination of  different miRNA profiles in 2 lines.

first: Ming

middle: m

first: Shu

middle: x

last: Yu


title: seq-SDQ4501_T09A5.8_FEM2_AD

summary:
modENCODE_submission_3917
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 T09A5.8 SDQ4501 (target is T09A5.8)


title: seq-AR0144_H3_144_N2_L3

summary:
modENCODE_submission_3564
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: L3 Larva; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  EXPERIMENTAL FACTORS: Developmental Stage L3 Larva; temp (temperature) 20 degree celsius; Strain N2; Antibody C. elegans  AR0144 H3 rabbit serum (target is histone H3)

first: Julie

last: Ahringer

first: Isabel

last: Latorre

first: Anne

last: Canonge


title: A global change in RNA Polymerase II pausing during the Drosophila midblastula transition [MNase-seq]

city: Kansas City

first: Julia

last: Zeitlinger

state: MO

country: USA

institute: Stowers Institute for Medical Research

summary: During animal development, a fertilized egg is initially under the control of maternal products and only starts zygotic transcription after several cell divisions. In animals such as Xenopus, zebrafish and Drosophila, a massive increase in zygotic transcription occurs during the mid-blastula transition (MBT), when cells shift from rapid, synchronous cell divisions without gap phases to prolonged asynchronous divisions. Before MBT, only a few so-called pre-MBT genes are expressed. How transcription is set up during these early stages is poorly understood. For example, paused RNA Polymerase (Pol II) is frequently found at developmental control genes in mammalian embryonic stem cells and Drosophila embryos but when Pol II pausing is first established in the embryo is unknown. We have analyzed the genome-wide Pol II occupancy during the maternal-to-zygotic transition in hand-staged Drosophila embryos. The results show that massive Pol II recruitment and pausing is established during MBT. The ~100 genes that are transcribed before MBT are particularly short, consistent with a need for rapid transcription during these early cell divisions. Remarkably, most of these genes are transcribed without Pol II pausing and this correlates with a TATA-enriched promoter type. This suggests that distinct strategies are used for activation in the early Drosophila embryo and this may reflect general dynamic properties of promoters used throughout development.

overall_design: Mnase-seq in staged Drosophila embryos

first: Kai

last: Chen

first: Jeff

last: Johnston

first: Wanqing

last: Shao

first: Sam

last: Meier

first: Nina

last: Koenecke

first: Cindi

last: Staber


title: A global change in RNA Polymerase II pausing during the Drosophila midblastula transition [ChIP-seq]

overall_design: ChIP-seq for Pol II, TBP, H3K4me3, H3K27me3 and H3Ac in Drosophila embryos


title: ChIP-seq of TALE fusions

city: Cambridge

first: Eric

last: Mendenhall

state: MA

address: 7 CC

institute: Broad Institute

summary:
We present a strategy to investigate regulatory elements that leverages programmable reagents to selectively inactivate their endogenous chromatin state. The reagents, which comprise fusions between transcription activator- like effector (TALE) repeat domains and the LSD1 histone demethylase, efficiently remove enhancer-associated chromatin modifications from target loci, without affecting control regions. We find that inactivation of enhancer chromatin by these fusions frequently causes down- regulation of proximal genes. Our study demonstrates the potential of 'epigenome editing' tools to characterize a critical class of functional genomic elements.

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: ChIP-seq analysis of TALE-Fusion Proteins

middle: M

first: Bradley

middle: E

last: Bernstein


title: Alteration of the microRNA network during the progression of Alzheimer’s disease

status: Public on Jul 25 2013

city: Leuven

first: Pierre

last: Lau

address: 49 Herestraat

country: Belgium

institute: KUL-VIB

summary: We report the high-throughput profiling of microRNAs (miRNAs) from the prefrontal cortex of controls, early and late-stages Alzheimer's disease subjects. We show miRNA expression changes between the two groups and down-regulation of miR-132-3p in the late-stages group.

overall_design: Deep-sequencing of microiRNAs in 6 controls/early-stages and 6 late-stages Alzheimer's disease patients

first: Rekin's

last: Janky

first: Stein

last: Aerts

first: Bart

last: De Strooper


title: RNA-Guided Human Gene Activation by Cas9/CRISPR-Based Engineered Transcription Factors

city: Durham

first: Timothy

last: Reddy

state: NC

address: 2347 CIEMAS, 101 Science Drive

department: Department of Biostatistics & Bioinformatics

institute: Duke University

type: Expression profiling by high throughput sequencing

summary: Synthetic transcription factors can be applied in many areas of biotechnology, medicine, and basic research.  In contrast to current methods based on engineering new DNA-binding proteins, we show that Cas9 fused to a transcriptional activation domain can be targeted by combinations of guide RNA molecules to induce the expression of endogenous human genes. This simple approach for targeted gene activation circumvents the need for engineering new proteins and will enable widespread synthetic gene regulation.

overall_design: HEK293T cells were transfected with plasmid expressing Cas9-VP64 fusion protein and a guide RNA. As a control, empty guide RNA was transfected. Gene expression was then measured using mRNA-seq, and differential expression calculated using DESeq. All experiments were performed in biological duplicates or triplicates.

first: Pablo

last: Perez-Pinera

first: Daniel

middle: D

last: Kocak

first: Christopher

last: Vockley

first: Andrew

middle: F

last: Adler

first: David

middle: G

last: Ousterout

first: Ami

last: Kabadi

first: Pratiksha

middle: I

last: Thakore

first: Lauren

middle: R

last: Polstein

first: Katherine

middle: A

last: Glass

first: Kam

middle: W

last: Leong

first: Farshid

last: Guilak

first: Gregory

last: Crawford

first: Charles

last: Gersbach


title: The yeast Snt2 protein helps coordinate the transcriptional response to hydrogen-peroxide mediated oxidative stress (rapamycin or DMSO)

status: Public on Jul 24 2013

city: New York

last: Allis

state: NY

address: 1230 York Ave Box 78

department: Laboratory of Chromatin Biology and Epigenetics

institute: The Rockefeller University

summary: Snt2 is a yeast chromatin-interacting protein whose function has not been well characterized, that was recently shown to associate with Ecm5 and the Rpd3 deacetylase. Using chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq), we show that in response to H2O2, Snt2 and Ecm5 colocalize to promoters of genes involved in various aspects of the environmental stress response. By integrating these ChIP-seq results with expression analysis, we identify a key set of target genes that require Snt2 for proper expression after H2O2 stress. Finally, by mapping Snt2 and Ecm5 localization before and after rapamycin treatment, we identify a subset of H2O2-specific Snt2 and Ecm5 target promoters that are also targeted in response to rapamycin. Our results establish a function for Snt2 in regulating transcriptional changes in response to oxidative stress, and suggest Snt2 may have a role in additional stress pathways.

overall_design: Crosslinking ChIP analysis to identify sites of Snt2 or Ecm5 genomic localization before, 0.5 hours after, or 4 hours after treatment with rapamycin (final concentration 5 nM) or with DMSO as a control. Snt2 and Ecm5 were genomically tagged with a 13Myc tag at their C termini. ChIPs were performed using a Myc antibody on either Snt2-Myc or Ecm5-Myc strains, or on untagged wildtype strain (BY4741) as a control. Inputs and ChIPs from untagged strain were sequenced as controls.

first: Lindsey

last: Baker

first: Scott

last: Dewell

first: Deyou

last: Zheng

first: C

first: Beatrix

last: Ueberheide

first: Brian

middle: T

last: Chait


title: A global change in RNA Polymerase II pausing during the Drosophila midblastula transition

first: Julia

last: Zeitlinger

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

overall_design: Refer to individual Series

first: Kai

last: Chen

first: Jeff

last: Johnston

first: Wanqing

last: Shao

first: Samuel

last: Meier

first: Cynthia

last: Staber


title: The yeast Snt2 protein helps coordinate the transcriptional response to hydrogen-peroxide mediated oxidative stress (RNA-seq)

first: David

overall_design: RNA-seq analysis to look at gene expression levels in wild-type, snt2 deletion, or ecm5 deletion strains before or 0.5 hours after treatment with H2O2 (final concentration 0.4 mM). This sequencing was done on biological triplicate samples.


title: The yeast Snt2 protein helps coordinate the transcriptional response to hydrogen-peroxide mediated oxidative stress


title: Quantitative analysis of proliferative and Ras-induced senescent human primary fibroblasts transcriptomes

city: Illkirch

first: Tao

last: YE

address: 1 rue Laurent Fries

country: France

institute: IGBMC (CNRS/INSERM/UDS)

summary: The goals of this study is to analyse transcriptionnal changes  in senescent cells and to compare them with ChIPseq data for several histones marks and proteins of the SUMO machinery

overall_design: mRNA profiling of proliferative versus Ras-induced senescent humain primary fibroblasts 5 days post-infection

first: Hélène

last: Neyret-Kahn

first: Moussa

last: Benhamed

last: Ye

first: Stéphanie

last: Le Gras

first: Pierre

last: Lapaquette

first: Maia

last: Ouspenskaia

first: Mary

last: Dasso

first: Jacob

last: Seeler

first: Irwin

last: Davidson

first: Anne

last: Dejean


title: The yeast Snt2 protein helps coordinate the transcriptional response to hydrogen-peroxide mediated oxidative stress (H2O2)

last: Allis

overall_design: Crosslinking ChIP analysis to identify sites of Snt2 or Ecm5 genomic localization before, 0.5 hours after, or 4 hours after treatment with H2O2 (final concentration 0.4 mM). Snt2 and Ecm5 were genomically tagged with a 13Myc tag at their C termini. ChIPs were performed using a Myc antibody on either Snt2-Myc or Ecm5-Myc strains, or on an untagged wildtype strain (BY4741) as a control. Inputs and ChIPs from untagged strain were sequenced as controls.

first: Lindsey

last: Baker

first: Scott

last: Dewell

first: Deyou

last: Zheng

first: C

first: Beatrix

last: Ueberheide

first: Brian

last: Chait


title: Genome wide occupancy of SUMO machinery in proliferative and Ras-induced senescent human primary fibroblasts

last: YE

summary: Transcription factors represent one of the largest groups of proteins regulated by SUMO, and their modification has generally been correlated with transcriptional repression. However, as most of the studies focus on specific sumoylated transcriptional regulators, the distribution and global role of SUMO on chromatin in relation to transcription regulation remain largely unknown. To investigate this role, we determined the occupancy of SUMO machinery proteins on chromatin by ChIP coupled to sequencing in human primary cells.

overall_design: Examination of 3 histone modifications, Polymerase II, SUMO1, SUMO2, Ubc9 and PIASy in proliferative and Ras-induced senescent fibroblasts.


title: SUMO is an Integral and Instructive Component of Chromatin in Cell Growth and Senescence


title: RNA-sequencing of the human milk fat layer during colostrum, transitional, and mature stages of lactation

status: Public on Jul 22 2013

city: Davis

first: Danielle

last: Lemay

state: CA

address: 451 Health Sciences Dr

department: Genome Center

institute: University of California Davis

summary: Human milk fat globules, by enveloping cell contents during their secretion into milk, are a rich source of mammary cell RNA. Here, we pair this non-invasive mRNA source with RNA sequencing technology to probe the milk fat layer transcriptome during three stages of lactation: colostral, transitional, and mature milk production. We find that transcriptional profiles cluster not by postpartum day, but by milk Na:K ratio, indicating that women sampled during the same postpartum time frame could be at markedly different stages of gene expression. Each stage of lactation is characterized by a dynamic range (105-fold) in transcript abundances not previously observed with microarray technology. We discovered that transcripts for isoferritins and cathepsins are strikingly abundant during colostrum production, highlighting the potential importance of these proteins for neonatal health. Two transcripts, encoding β-casein (CSN2) and a-lactalbumin (LALBA), make up 45% of the total pool of mRNA in mature lactation. Genes significantly expressed across all stages of lactation are associated with making, modifying, transporting, and packaging milk proteins. Stage-specific transcripts are associated with immune defense during the colostral stage, up-regulation of the machinery needed for milk protein synthesis during the transitional stage, and the production of lipids during mature lactation. We observed strong modulation of key genes involved in lactose synthesis and insulin signaling. In particular, PTPRF may serve as a biomarker linking insulin resistance with insufficient milk supply. This study provides the methodology and reference data set to enable future targeted research on the physiological contributors to sub-optimal lactation in humans.

overall_design: Milk fat mRNA profiles were generated from Day 2 and mature milk samples obtained from lactating mothers

first: Laurie

last: Nommsen-Rivers


title: Inducing pluripotency from mouse somatic cells by small-molecule compounds [RNA-Seq]

city: beijing

first: chun

last: liu

state: beijing

address: beijing

institute: Peking University

summary: Pluripotent stem cells can be induced from somatic cells, providing an unlimited cell resource for regenerative medicine. However, genetic manipulation and difficult-to-manufacture strategies used in reprogramming limit their clinical applications. Here, we show pluripotency can be induced from mouse somatic cells by specific small-molecule compounds. The completely chemically-induced pluripotent stem cells (CiPSCs) can be stably maintained in embryonic stem cell (ESC) culture medium and resemble ESCs in terms of their gene expression profiles, epigenetic status, and potential for differentiation and germline transmission. These findings suggest that exogenous master genes are dispensable for cell fate reprogramming and pave the way for the clinical application of somatic reprogramming techniques. Chemicals' acronym: V, VPA; C, CHIR; 6, 616452; T, tranylcypromine; F, FSK; Z, DZNep; P, PGE2; R, RG108; S, SRT1720; M, 2-Me-5HT; D, D4476; B, Sodium butyrate.

overall_design: mRNA expression analysis of mouse embryonic fibroblasts (MEFs), GFP- cells, GFP+ clusters,GFP+ colonies, embryonic stem cells (ESCs) and CiPSCs by RNA sequencing.

first: Pingping

last: Hou

first: Yanqin

last: Li

first: Xu

last: Zhang

first: Chun

last: Liu

first: Jingyang

last: Guan

first: Honggang

first: Yang

last: Zhao

first: Hongkui

last: Deng


title: Inducing pluripotency from mouse somatic cells by small-molecule compounds

type: Genome variation profiling by genome tiling array


title: NSun2-mediated cytosine-5 methylation in Vault non-coding RNA determines its processing into small RNAs [iCLIP]

status: Public on Jul 23 2013

city: St Louis

first: Sabine

last: Dietmann

address: 4565 McKinley Avenue

institute: Washington University School of Medicine

summary: Autosomal-recessive loss of the NSUN2 gene has been recently identified as a causative link to intellectual disability disorders in humans. NSun2 is an RNA methyltransferase modifying cytosine-5 in transfer RNAs (tRNA). Whether NSun2 methylates additional RNA species is currently debated. Here, we adapted the individual-nucleotide resolution UV cross-linking and immunoprecipitation method (iCLIP) to identify NSun2-mediated methylation in RNA transcriptome. We confirm site-specific methylation in tRNA and identify messenger and non-coding RNAs as potential methylation targets for NSun2. Using RNA bisulfite sequencing we establish Vault non-coding RNAs as novel substrates for NSun2 and identified six cytosine-5 methylated sites. Furthermore, we show that loss of cytosine-5 methylation in Vault RNAs causes aberrant processing into argonaute-associating small RNA fragments (svRNA). Thus, impaired Vault non-coding RNA processing may be an important contributor to the etiology of NSUN2-deficieny human disorders.

overall_design: Identification of Nsun2 targets by miCLIP in Embryonic kidney (HEK293) cells

first: Shobbir

last: Hussain


title: NSun2-mediated cytosine-5 methylation in Vault non-coding RNA determines its processing into small RNAs


title: H3K27me3 is maintained at a reduced level in Suz12(Bgal/Bgal) ESCs [RNA-Seq]

last: Boyer

address: 77 Massachusetts Avenue

department: Biology

institute: Massachusetts Institute of Technology

summary: Suz12(Bgal/Bgal) ESCs express a truncated form of Suz12 fused to Beta-galactosidase. These cells maintain a reduced level of H3K27me3 despite this mutation to a core component of PRC2, unlike Eed-/- ESCs whose H3K27me3 is ablated.

overall_design: RNA-seq was performed in wild type and Suz12(Bgal/Bgal) ESCs, here used to demonstrate the coverage of the Suz12 gene in mRNA reads.

first: Seraphim

last: Thornton


title: NSun2-mediated cytosine-5 methylation in Vault non-coding RNA determines its processing into small RNAs [RNA-seq]

overall_design: mRNA-seq in Embryonic kidney (HEK293) cells transfected with siRNA against Nsun2 vs control


title: RNA-seq-based analysis of the physiologic cold shock-induced changes in Moraxella catarrhalis gene expression

city: Bern

first: Stefan

last: Wyder

address: Murtenstrasse 31

department: Dpt. Clinical Research

country: Switzerland

institute: University of Bern

summary:
Background: Moraxella catarrhalis, a major nasopharyngeal pathogen of the human respiratory tract, is exposed to rapid downshifts of environmental temperature when humans breathe cold air. The prevalence of pharyngeal colonization and respiratory tract infections caused by M. catarrhalis is greatest in winter. We investigated how M. catarrhalis uses the physiologic exposure to cold air to regulate pivotal survival systems that may contribute to M. catarrhalis virulence.
Results: In this study we used the RNA-seq techniques to quantitatively catalogue the transcriptome of M. catarrhalis exposed to a 26°C cold shock or to continuous growth at 37°C. Validation of RNA-seq data using quantitative RT-PCR analysis demonstrated the RNA-seq results to be highly reliable. We observed that a 26°C cold shock induces the expression of genes that in other bacteria have been related to virulence: a strong induction was observed for genes involved in high affinity phosphate transport and iron acquisition, indicating that M. catarrhalis makes a better use of both phosphate and iron resources after exposure to cold shock. We detected the induction of genes involved in nitrogen metabolism, as well as several outer membrane proteins, including ompA, m35-like porin and multidrug efflux pump (acrAB) indicating that M. catarrhalis remodels its membrane components in response to downshift of temperature. Furthermore, we demonstrate that a 26°C cold shock enhances the induction of genes encoding the type IV pili that are essential for natural transformation, and increases the genetic competence of M. catarrhalis, which may facilitate the rapid spread and acquisition of novel virulence-associated genes.

overall_design: mRNA profiles of Moraxella catarrhalis were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000.

first: Violeta

last: Spaniol

first: Christoph

last: Aebi


title: The transcriptomic basis of oviposition behaviour in the parasitoid wasp Nasonia vitripennis

city: Wageningen

first: Bart

last: Pannebakker

address: Droevendaalsesteeg 1

country: Netherlands

institute: Wageningen University

summary: For many behaviours studied at the phenotypic level, we have little or no idea of where to start searching for “candidate” genes: the transcriptome provides such a starting point. Here we consider transcriptomic changes associated with oviposition in the parasitoid wasp Nasonia vitripennis. Oviposition is a key behaviour, as females are faced with a variety of decisions that will impact offspring fitness. These include choosing between hosts of differing quality, as well as deciding on clutch size and offspring sex ratio. We compared the whole-body transcriptomes of resting or ovipositing female Nasonia using a “DEEP-Sage” gene expression approach on the Illumina sequencing platform.

overall_design: Single 2-day old mated Nasonia vitripennis females (ASymC strain) were isolated in a glass vial and provided with a single host to produce F1 daughters. Eight 2-day old mated F1 females were subsequently provided with three hosts to produce the F2 test females. We randomly selected one host from each F1 female, and isolated 16 2-day old mated F2 test females in glass tubes, of which eight were randomly allocated to the oviposition treatment and eight to the resting treatment. We provided the test females with a single host for 24 hours as pre-treatment to facilitate egg development. We then discarded the pre-treatment hosts and gave each female a piece of chromatography paper soaked in honey solution for a further 24 hours. For the experiment, we transferred the females to 1.5 mL Eppendorf tubes that contained a single host for the oviposition experiment, or were empty for the resting treatment. After 60 mins, females were flash-frozen in liquid nitrogen and stored on dry-ice until the addition of RNAlater-ICE (Ambion, Austin, TX, USA) after which they were transferred to -20C. All females in the oviposition treatment were observed to have commenced ovipositing. We pooled the F2 test females from each F1 mother according to treatment, generating a total of eight pooled samples per treatment (consisting of 8 females per pool) for RNA isolation and sequencing.

first: Urmi

last: Trivedi

first: Mark

last: Blaxter

first: Rebekah

last: Watt

first: David

last: Shuker


title: H3K27me3 is maintained at a reduced level in Suz12(Bgal/Bgal) ESCs [ChIP-Seq]

first: Laurie

overall_design: Two ESC lines mutant in genes of core components of Polycomb Repressive Complex 2 were assessed for H3K27me3 by ChIP-seq, as compared to a wild type ESC line.


title: H3K27me3 is maintained at a reduced level in Suz12(Bgal/Bgal) ESCs


title: The pluripotent genome in three dimensions is shaped around pluripotency factors

city: Utrecht

first: Elzo

last: de Wit

address: Uppsalalaan 8

institute: Hubrecht Institute

summary: It is becoming increasingly clear that the shape of the genome importantly influences transcription regulation. Pluripotent stem cells (PSCs) such as embryonic stem cells (ESCs) were recently shown to organize their chromosomes into topological domains that are largely invariant between cell types. Here, we applied 4C technology and combined ChIP-seq with Hi-C data to demonstrate that inactive chromatin is unusually disorganized in PSC nuclei. We show that gene promoters engage in contacts between topological domains in a largely tissue-independent manner while enhancers have a more tissue-restricted interaction profile. Most strikingly, genomic clusters of pluripotency factor binding sites find each other very efficiently, in a manner that is strictly PSC-specific, dependent on the presence of Oct4 and Nanog protein and inducible upon artificial recruitment of Nanog to a selected chromosomal site. We conclude that pluripotent stem cells have a unique higher-order genome structure shaped by pluripotency factors. We speculate that this interactome enhances the robustness of the pluripotent state.

overall_design: 4C-seq was performed on a range of viewpoints in pluripotent (2x ESC, iPSC) and differentiated (neural precursor cells and astrocytes) cell lines.

first: Britta

last: Bouwman

first: Petra

last: Klous

first: Erik

last: Splinter

first: Maaike

last: Welling

first: Niels

last: Geijsen

first: Wouter

last: de Laat

first: Yun

last: Zhu

first: Marjon

last: Verstegen

first: Elphege

last: Nora

first: Edith

last: Heard

first: Nicola

last: Festuccia

first: Ian

last: Chambers

first: Peter

last: Krijger

first: Raymond

last: Poot


title: Gene expression analysis of lung fibroblasts in bleomycin-induced pulmonary fibrosis

city: Tokyo

first: Tatsuya

last: Tsukui

address: 7-3-1, Hongo, Bunkyo-ku

department: Graduate School of Medicine

country: Japan

institute: The University of Tokyo

summary: We conducted fibroblast-specific transcriptome analysis by next generation sequencing in order to investigate qualitative change and activation signatures of lung fibroblasts in bleomycin-induced pulmonary fibrosis. Lung fibroblasts were identified by using reporter mice of collagen-α2(I), in which collagen I-producing fibroblasts were labeled with EGFP. Lungs were dissociated with protease sollution, and single cell suspension were stained with lineage markers (Ter119, CD45, CD31, EpCAM). Lineage- GFP+ cells were sorted out and mRNA was collected. Using serial analysis of gene expression (SAGE) method, we identified 2,973,937 SAGE tags (1,080,798 tags from saline-treated GFP+ fibroblasts and 1,893,139 tags from bleomycin-treated GFP+ fibroblasts). We found that genes related to extracellular matrix construction were highly up-regulated in fibroblasts from belomycin-treated lungs. Moreover, an analysis of mRNA profiles revealed biological functions such as proliferation, invasion, adhesion, and migration were promoted in fibroblasts from bleomycin-treated lung, which recapitulated the role of fibroblasts in the fibrogenesis. These fibroblast-specific gene expression profiles will be important notions in future fibrosis studies.

overall_design: mRNA profiles of Lung fibroblasts from 3 mice at day 14 after saline or bleomycin treatment.

first: Satoshi

last: Ueha

first: Shin-ichi

last: Hashimoto

first: Kenshiro

last: Oshima

first: Masahira

last: Hattori

first: Kouji

last: Matsushima


title: DNA Methylome in Human Peripheral Blood Monocytes

city: New Orleans

first: Chuan

last: Qiu

state: LA

address: 1440 Canal St.

department: Department of Biostatistics and Bioinformatics

institute: Tulane University School of Public Health & Tropical Medicine

type: Methylation profiling by high throughput sequencing

summary:
Purpose: We characterized genome-wide DNA methylation profiles (methylome) in purified peripheral blood monocytes (PBMs) from 18 healthy postmenopausal Caucasian females aged 50-56 years.
Methods: DNA methylome of Human Peripheral Blood Monocytes were generated by methylated DNA immunoprecipitation combined with high-throughput sequencing (MeDIP-seq), using Illumina GAIIx. The sequence reads that passed quality filters were analyzed using MEDIPS package. Targeted methylation validation analysis was performed by using MassARRAY EpiTYPER assays. Genome-wide gene expression profiles have been obtained for 7 of the 18 subjects by using Affymetrix 1.0 Human Exon ST arrays following the manufacturer's recommended protocols.
Results: Using MeDIP-seq,a total of approximately 283 million reads were uniquely aligned to human genome (Build NCBI37, HG19), resulting in average ~16 million uniquely aligned high quality reads per sample. Distinct patterns were revealed at different genomic features. For instance, promoters were commonly (~58%) found to be unmethylated; whereas protein coding regions were largely (~84%) methylated. We found that approximately 24% CpG islands (CGIs) were highly methylated in PBMs. Further characterization of CGIs with respect to their relative locations to RefSeq genes revealed that the highly methylated CGIs were largely enriched (~89%) in CGIs located in gene bodies and intergenic regions. By integration of the methylome data with genome-wide PBM gene expression data, we found negative correlation between promoter methylation levels and gene transcription levels when comparing groups of genes with different expression levels, and this relationship was consistently observed across promoters with high to low CpG densities. Furthermore, we observed a modest but significant excess (permutation p<0.0001) of genes showing negative correlation between inter-individual promoter methylation and transcription levels, particularly for genes associated with CpG-rich promoters. Across the 18 individual PBM methylomes, we also identified genomic regions that were constitutively highly methylated in PBMs as well as regions showing large inter-individual variability.
Conclusions: This study represents a comprehensive analysis of the PBM methylome and our data provides a valuable resource for future epigenomic and multi-omic studies exploring biological and disease-related regulatory mechanisms in PBMs.

overall_design: DNA methylome of human peripheral blood monocytes were generated by MeDIP-seq, using Illumina GAIIx.

first: Hui

last: Shen

first: Hongwen

last: Deng


title: Differentiated Truncation and Uridylation Patterns of miRNAs in Arabidopsis and Rice hen1 Mutants Suggest miRNAs May Re-program RISC

city: St. Louis

first: Blake

middle: C.

last: Meyers

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

summary: miRNA levels depend on both biogenesis and turnover. The methyltransferase HEN1 stabilizes plant miRNAs, animal piRNAs, and siRNAs in both kingdoms via 3' terminal methylation. Loss of HEN1 in plants results in non-templated oligo-uridylation and accelerated degradation of miRNAs. In hen1 mutants from Arabidopsis and rice, we found that the patterns of miRNA truncation and uridylation differ substantially among miRNA families, but such patterns for the same miRNA are conserved between species. miR166 and miR163 are truncated predominantly to ~17 and ~16 nt, and subsequently recover via uridylation to approximately their original sizes, 21 and 24 nt, suggesting that in these cases miRNA truncation triggers uridylation. miR171 is untruncated but uridylated to 22 nt in hen1 mutants, gaining the ability to trigger production of phased, secondary siRNAs. Truncated and tailed variants were bound by ARGONAUTE1 (AGO1) in hen1, implying that these events occur while miRNAs are still bound by AGO1. Unexpectedly, a portion of miR158 in wildtype remains unmethylated and thus subject to uridylation and destabilization, suggesting that plants naturally utilize miRNA methylation to modulate miRNA accumulation. Our results suggest that the AGO1-containing RISC complex may undergo programming to reflect each bound miRNA, determining a defined, distinct decay destiny.

sample_organism:
Arabidopsis thaliana
Oryza sativa
Zea mays

overall_design: In this analysis, we sequenced sRNAs from two hen1 mutant alleles in Arabidopsis and three hen1 alleles in rice. In Arabidopsis, the strong hen1-1 allele in the Landsberg erecta (Ler) ecotype is the first hen1 mutant and emerged from an enhancer screen in the hua1-1/hua2-1 background, and hen1-8 in the Columbia (Col) background is a weak allele. In rice, WAVY LEAF1 (WAF1) is the ortholog of Arabidopsis HEN1, and two mutant alleles waf1-1 and waf1-2 each bear a single-base substitution leading to a premature stop codon in the second exon and a non-functional splicing site of the fourth intron, respectively. We identified a third mutant allele of the rice HEN1 gene (Oshen1-3 from the Korean (POSTEC) rice T-DNA mutant population).

middle: C

first: Jixian

last: Zhai


title: Avoiding chromosome pathology when replication forks collide

city: Norwich

first: Conrad

last: Nieduszynski

address: Norwich Research Park

country: United Kingdom

institute: Earlham Institute

summary: Chromosome duplication normally initiates via the assembly of replication fork complexes at defined origins. DNA synthesis by any one fork is thought to cease when it meets another travelling in the opposite direction, at which stage the replication machinery may simply dissociate before the nascent strands are finally ligated. But what actually happens is not clear. Here we present evidence consistent with the idea that every fork collision has the potential to trigger re-replication of the already replicated DNA, thus posing a threat to genomic integrity. In Escherichia coli this threat is kept at bay by the RecG DNA translocase. Without RecG, replication initiates where forks meet, establishing new forks with the potential to sustain cell growth and division in the absence of an active origin. The studies reported raise the question of how eukaryotic and archaeal cells are able to exploit multiple origins for the duplication of each chromosome without any apparent ill effect from the consequent multiple fork collisions.

overall_design: Measurement of replication dynamics (marker frequency analysis; MFA) for E. coli strains, including wild-type and various mutants.

first: Christian

middle: J

last: Rudolph

first: Amy

middle: L

last: Upton

first: Anna

last: Stockum

first: Robert

last: Lloyd


title: Tight coordination of protein translation and heat shock factor 1 activation supports the anabolic malignant state

status: Public on Jul 21 2013

first: Marc

last: Mendillo

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

overall_design: Refer to individual Series


title: De novo sequencing of circulating microRNAs in locally advanced breast cancer

status: Public on Jul 20 2013

city: Duarte

first: Xiwei

last: Wu

address: 1500 E Duarte Rd

department: Molecular and Cellular Biology

institute: Beckman Research Institute

summary: MicroRNAs (miRNAs) have been recently detected in the circulation of cancer patients, where they are associated with clinical parameters. Discovery profiling of circulating small RNAs has not been previously reported in breast cancer (BC), and was carried out in this study to identify blood-based small RNA markers of BC clinical outcome.

overall_design: The pre-treatment sera of 42 stage II–III locally advanced and inflammatory BC patients who received neoadjuvant chemotherapy (NCT) followed by surgical tumor resection were analyzed for marker identification by deep sequencing all circulating small RNAs.

first: Shizhen

last: Wang


title: Small RNA expression in swi6 mutants or dcr1 delta fission yeast Schizosaccharomyces pombe

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

institute: FMI

summary: Small RNA expression in swi6 mutants, dcr1 delta, and wild type fission yeast Schizosaccharomcyces pombe

overall_design: wild type, swi6 mutant, and dcr1 delta mutant

first: Raghavendran

last: Kulasegaran-Shylini

first: Claudia

last: Keller

first: Yukiko

last: Shimada

first: Hans-Rudolf

last: Hotz

first: Kirsten

last: Jacobeit

last: Bühler

first: Dimosthenis

last: Gaidatzis


title: Gene expression profiling of zebrafish embryos at 5 days post fertilization

status: Public on Aug 01 2013

city: Leiden

first: Herman

middle: Pieter

last: Spaink

address: Einsteinweg 55

department: Institute of Biology

institute: Leiden University


summary: Genome wide map of heterochromatin state in fission yeast Schizosaccharomyces pombe via 4 different strains

overall_design: Examination of a single histone modification in 4 different fission yeast strains

first: Sophie

last: Dessus-Babus

last: Buehler


title: Genome-wide DNA methylation maps of Arabidopsis thaliana in two seasons

city: Beijing

first: Yu-Xian

last: Zhu

address: 5# Summer Palace Road

institute: College of life sciences, Peking University

summary: DNA methylation is involved in many biological processes during plant growth and development. Here, we report a novel annual growth rhythm that is found in cotton plants grown in different time-of-year. To further study this rhythm in other plants, we use Arabidopsis thaliana for genome-wide bisulfite sequencing.

overall_design: Two A. thaliana DNA samples were extracted from 20 days old whole plant in Feburary and August for bisulphite treatment and further Illumina sequencing.

first: Xiang

last: Jin

first: Qin

last: Li

first: Fangxing

last: Jia

first: Yuxian


title: Heterochromatin state in fission yeast Schizosaccharomyces pombe

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

first: Marc


title: Genome-wide mapping of SPDEF and ESR1 binding in MCF-7 cells (ChIP-seq)

status: Public on Jul 17 2013

city: Cambridge

first: Mauro

middle: Antonio

last: Alves Castro

address: Robinson Way

institute: Cambridge Research Institute

summary: Using a transcriptional network derived from 2000 breast cancer gene expression profiles we identify the master regulators (MRs) of FGFR2 signalling. To validate the identified regulons, we examined whether there was enrichment of TF binding near the transcription start sites (TSS) of genes found in the regulons of a particular MR.

overall_design: For ESR1 and SPDEF, ChIP-seq experiments were performed in MCF-7 cells, while existing data was analysed for FOXA1 (Hurtado et al. Nature Genetics, 43:27–33, 2010) and GATA3 (Theodorou, et al., Genome Res 23: 12-22, 2013). ChIP-seq experiments were performed on three biological replicates per each transcription factor. For each sample, 36bp single-end reads were obtained. Peak regions were identified in all ChIP-seq TF data sets using the peak caller algorithm MACS (Zhang et al., Genome Biology, 9(9):R137, 2008) with default parameters.

last: Castro

first: Michael

last: Fletcher

first: Ines

last: de Santiago

first: Florian

last: Markowetz

first: Kerstin

last: Meyer


title: Targeting H3K4 methylation as a therapeutic strategy for Huntington's disease (RNA-seq)

status: Public on Jul 18 2013

first: Christopher

last: Ng

state: Massachusetts

address: 77 Massachusetts Ave.

summary: Transcriptional dysregulation is an early feature of Huntington's disease (HD). We observed gene-specific changes in H3K4me3 at transcriptionally repressed promoters in R6/2 mouse and human HD brain. Genome-wide analysis showed a novel chromatin signature for this mark. Reducing the levels of the H3K4 demethylase SMCX/Jarid1c in primary neurons reversed down-regulation of key neuronal genes caused by mutant Huntingtin (Htt) expression. Finally, reduction of SMCX/Jarid1c in primary neurons from BACHD mice or the single Jarid1 in a Drosophila HD model was protective. Therefore, targeting this epigenetic signature may be an effective strategy to ameliorate the consequences of HD.

overall_design: mRNA-seq in wild type and R6/2 cortex and striatum at 8 and 12 weeks.

first: Ernest

last: Fraenkel

first: Malini

last: Vashishtha

first: Theresa

last: Gipson

first: Leslie

last: Thompson

first: David

last: Housman


title: Transcriptomic profiling of L-rhamnose utilization in Lmo0753 deletion mutant of Listeria monocytogenes EGDe from human foodborne outbreak associated lineage LII

city: Bedford Park

first: Joelle

middle: K

last: Salazar

state: IL

address: 6502 S Archer Rd

institute: Illinois Institute of Technololgy

summary:
Among the three major genetic lineages of L. monocytogenes (i.e. LI, LII, and LIII), LI and LII are predominantly associated with foodborne listeriosis outbreaks, whereas LIII is rarely implicated in human infections. In a previous study, we identified a Crp/Fnr family transcription factor lmo0753 that was highly specific to outbreak-associated LI and LII but absent from LIII. Lmo0753 shares two conserved functional domains including a DNA-binding domain with the well-characterized master virulence regulator PrfA in L. monocytogenes. In this study, we constructed a lmo0753 deletion and complementation mutants of the fully sequenced L. monocytogenes LII strain EGDe. We found that deletion of lmo0753 led to the loss of L-rhamnose utilization in EGDe. Transcriptomic comparison of the EGDe lmo0753 deletion mutant and the wild type incubated in phenol-red medium containing L-rhamnose as the sole carbon source revealed 126 (4.5%) and 546 (19.5%) out of 2,798 genes in the EGDe genome that were up- and down-regulated for more than 2-fold, respectively. Genes involved in biotin biosynthesis, general stress response and rhamnose metabolism were shown to be differentially regulated by Lmo0753.  Findings from this study may partially explain why LIII of L. monocytogenes is underrepresented in the environment and rarely associated with human listeriosis outbreaks due to the inability of rhamnose utilization.

We report the transcriptomic profile of L. monocytogenes Δlmo0753 LII strain (EGDe) in broth media with L-rhamnose as the sole carbon source.

overall_design: Examination of deletion of Lmo0753 on L-rhamnose utilization in L. monocytogenes. Two biological replicates per WT and Δlmo0753.

first: Wei

last: Zhang


title: Saccharopolyspora erythraea RNA-seq

status: Public on Jul 16 2013

city: Shanghai

first: Weibing

last: Liu

address: Meilong Road 130

institute: East China University Of Science And Technology

summary: We report the high-throughput profiling of saccharopolyspora erythraea including a industrial strain HL3168 E3 and a wild-type strain NRRL23338. The aim was to evaluate the difference in expression of sRNA predicted in silico related to secondary metabolites in Saccharopolyspora erythraea.

overall_design: Comparison of the gene expression difference in 2 Saccharopolyspora erythraea strains.

first: Bangce

last: Ye


title: Global signatures of protein binding on structural RNAs in Saccharomyces cerevisiae

status: Public on Jul 15 2013

city: Baltimore

first: Mallory

middle: Ann

last: Freeberg

state: MD

address: 3400 N Charles St

department: Department of Biology

institute: Johns Hopkins University

summary: Protein binding is essential to the transport, decay and regulation of almost all RNA molecules. However, the structural preference of protein binding on RNAs and their cellelar functions and dynamics upon changing environmental condictions are poorly understood. Here, we integrated various high-throughput data and introduced a computational framework to describe the global interactions between RNA binding proteins (RBPs) and structured RNAs in yeast at single-nucleotide resolution. We found that on average, in terms of percent total lengths, ~15% of mRNA untranslated regions (UTRs), ~37% of canonical ncRNAs and ~11% of long ncRNA (lncRNAs) are bound by proteins. The RBP binding sites, in general, tend to occur at single-stranded loops, with evolutionarily conserved signatures, and often facilitate a specific RNA structure conformation in vivo. We found that four nucleotide modifications of tRNA are significantly associated with RBP binding. We also identified various structural motifs bound by RBPs in the UTRs of mRNAs, associated with localization, degradation and stress responces. Moreover, we identified >200 novel lncRNAs bound by RBPs, and about half of them contain conserved secondary structures. We present the first ensemble pattern of RBP binding sites in the structured noncoding regions of a eukaryotic genome, emphasizing their structural context and cellular functions.

overall_design:
Duplicate gPAR-CLIP libraries were sequenced from yeast strains for each of three conditions: log-phase growth, growth after 2 hour glucose starvation, and growth after 2 hour nitrogen starvation. polyA RNAs were isolated for all conditions.
Total RNA were isolated from log phase growth conditions. Sucrose gradient fractionation was performed: some RNAs were isolated from the "light" fraction (lighter than 40S ribosome) and some from the "heavy" fraction. gPAR-CLIP libraries were used to determine regions of RNA bound by proteins.

first: Ting

last: Han

first: Yu-Cheng

last: Yang

first: Zhi

last: Lu


title: Master regulators of FGFR2 signalling and breast cancer risk

first: Mauro

last: Alves Castro


title: Response of Burkholderia cenocepacia H111 to micro-oxia

city: Zürich

first: Gabriella

last: Pessi

address: Winterthurerstrasse 190

institute: University of Zürich

summary: B. cenocepacia is an opportunistic human pathogen that is particularly problematic for patients suffering from cystic fibrosis (CF). In the CF lung, bacteria grow to high densities within the viscous mucus that is limited in oxygen. Pseudomonas aeruginosa, the dominant pathogen in CF patients, is known to grow and survive under oxygen-limited to anaerobic conditions by using micro-oxic respiration, denitrification and fermentative pathways. In contrast, inspection of the genome sequences of available B. cenocepacia strains suggested that B. cenocepacia is an obligate aerobic and non-fermenting bacterium. In accordance with the bioinformatics analysis, we observed that B. cenocepacia H111 is able to grow with as little as 0.1% O2 but not under strictly anoxic conditions. Phenotypic analyses revealed that H111 produced larger amounts of biofilm, pellicle and proteases under micro-oxic conditions (0.5% - 5% O2, i.e. conditions that mimic those encountered in CF lung infection), and was more resistant to several antibiotics. RNA-Seq and shotgun proteomics analyses of cultures of B. cenocepacia H111 grown under micro-oxic and aerobic conditions showed up-regulation of genes involved in the synthesis of the exopolysaccharide (EPS) cepacian as well as several proteases, two isocitrate lyases and other genes potentially important for life in micro-oxia.

overall_design: Oxygen regulation in Burkholderia cenocepacia was investigated using RNA-Seq of cells grown under aerobic or micro-oxic conditions.

first: Rubina

last: Braunwalder

first: Alexander

last: Grunau

first: Ulrich

last: Omasits

first: Christian

middle: H

last: Ahrens

first: Leo

last: Eberl


title: Targeting H3K4 methylation as a therapeutic strategy for Huntington's disease (ChIP-seq)

first: Christopher

last: Ng

institute: Massachusetts Institute of Technology

overall_design: ChIP-seq for H3K4me3 in wild type and R6/2 cortex and striatum at 8 and 12 weeks.

first: Ferah

last: Yildirim

first: Malini

last: Vashishtha

first: Theresa

last: Gipson

first: Leslie

middle: M

last: Thompson

first: Ernest

last: Fraenkel


title: Genome-wide nucleosome, TFIIIC and TFIIIB occupancies in Saccharomyces cerevisiae

city: Bethesda

first: Nagarajavel

last: Vivekananthan

state: Maryland

address: 9500 Rockville Pike, Buld 6A/Rm 2A14

department: NICHD

institute: National Institutes of Health

summary: Paired-end sequencing study of nucleosomes and immuno-precipitated Tfc1 and Brf1 complexes from MNase-digested nuclei.

overall_design: Nucleosomal DNA, input DNA and DNA from immunopurified TFIIIB and TFIIIC complexes (IP) were subjected to paired-end sequencing.

first: Vivekananthan

last: Nagarajavel

first: David

last: Clark


title: High throughput sequencing of immunoglobulin (Ig) heavy (IgH) and light (IgL) chain repertoires

city: Boston

first: Frederick

last: Alt

address: 1 Blackfan Circle

department: Program in Cellular and Molecular Medicine

institute: Boston Children's Hospital

summary: We used 454 sequencing to assess the repertoire of B cell subsets from bone marrow, spleen, and small intestinal lamina propria from two mouse strains. We used a RAG2-GFP reporter mouse strain (129Sve background) to isolate CD19+ RAG2+ B lineage cells from bone marrow and small intestinal lamina propria and total splenic B cells. We used 5' RACE to amplify cDNA libraries using primers specific for the mu constant region of IgH and the Ig kappa constant region. We also used this technique to analyze total B cell libraries from Swiss Webster germ-free mice to compare to littermate controls that were cohoused with regular specific pathogen free (SPF) mice for 7 days.

overall_design: Examination of the Ig kappa repertoire and IgH repertoire in RAG2+ bone marrow B lineage cells compared to RAG2+ small intestinal lamina propria B lineage cells or total splenic B cells.  There are 8 (Ig kappa) or 4 (IgH) independent experiments comparing repertoires in RAG2-GFP mice. Each experiment in RAG2-GFP+ mice consisted of a pool of 8-12 mice. There are 3 experiments comparing germ-free to colonized mouse total B cell repertoires, each consisting of one mouse per condition.

first: Duane

last: Wesemann

first: Andrew

middle: P

last: Portuguese

first: Robin

last: Meyers

first: Michael

last: Gallagher

first: Kendra

last: Cluff-Jones

first: Jennifer

first: Rohit

last: Panchakshari

first: Scott

last: Rodig

first: Thomas

middle: B

last: Kepler


title: Targeting H3K4 methylation as a therapeutic strategy for Huntington's disease

first: Christopher

last: Ng


title: RNA profiling of Synechococcus sp. PCC 7002 exposed to acrylic acid

status: Public on Jul 19 2013

city: Madison

first: Brian

last: Pfleger

state: WI

address: 1415 Engineering Dr

department: Chemical and Biological Engineering

institute: University of Wisconsin-Madison

summary: Cyanobacteria are valuable organisms for studying the physiology of photosynthesis and carbon fixation as well as metabolic engineering for the production of fuels and chemicals. This work describes a novel counter selection method for the cyanobacterium Synechococcus sp. PCC 7002 based on organic acid toxicity. The organic acids acrylate, 3-hydroxypropionate, and propionate were shown to be inhibitory towards PCC 7002 and other cyanobacteria at low concentrations. Inhibition was overcome by a loss of function mutation in the gene acsA. Loss of AcsA function was used as a basis for an acrylate counter selection method.  DNA fragments of interest were inserted into the acsA locus and strains harboring the insertion were isolated on selective medium containing acrylate. This methodology was also used to introduce DNA fragments into a pseudogene, glpK. Application of this method will allow for more advanced genetics and engineering studies in PCC 7002 including the construction of markerless gene deletions and insertions. The acrylate counter-selection could be applied to other cyanobacterial species where AcsA activity confers acrylate sensitivity (e.g. Synechocystis sp. PCC 6803).

overall_design: Cultures were grown in medium modified with 5mM acrylic acid at pH 8 and compared to cultures grown in unmodified medium. Samples were processed in duplicate.

first: Matthew

last: Begemann

middle: F


title: Unraveling the molecular basis of temperature-dependent genetic regulation in Penicillium marneffei

city: College Station

first: James

last: Cai

state: TX

address: 4458 TAMU

department: VIBS

institute: Texas A&M University

summary: Comparative analysis of transcriptome of Penicillium marneffei PM1 grown at 25°C and 37°C

overall_design: Penicillium marneffei strain PM1 was pre-cultured at  25°C and 37°C for two weeks on Sabouraud's Dextrose Agar (SDA). Messenger RNAs were then isolated from one-week 25°C and 37°C cultures and sequenced with Illumina by BGI America. Two replicates.

first: Ence

last: Yang

first: Gang

last: Wang


title: Genome-wide maps of Nup98 binding in human embryonic stem cells, neural progenitors, neuron cells and lung fibroblasts

city: La Jolla

first: William

middle: Harvey

last: Light

state: California

address: 10010 N Torrey Pines Rd

department: MCBL-Z

institute: The Salk Institute for Biological Studies

summary: Recent evidence suggests that nucleoporins, well known components that control nucleo-cytoplasmic trafficking, have wide-ranging functions in developmental gene regulation that potentially extend beyond their role in nuclear transport. Whether the unexpected role of nuclear pore proteins in transcription regulation, which initially has been described in fungi and flies, also applies to human cells is unknown. Here we show at a genome-wide level that the nuclear pore protein NUP98 associates with developmentally regulated genes active during human embryonic stem cell differentiation.

overall_design: Examination of Nup98 binding using multiple Nup98 antibodies in four cell types, three of which are related by direct lineage.

first: Yun

last: Liang

first: Martin

last: Hetzer


title: Adult Murine Interstitial Cells of Cajal (ICC) and Small Intestine (Sm Int) Somatic piRNA-like RNA (pilRNA)

city: Reno

first: Nicole

last: Ortogero

state: Nevada

address: 1664 N. Virginia St

department: Physiology and Cell Biology

institute: University of Nevada, Reno

summary: This study annotates the NGS reads in ICC and Sm Int sncRNA libraries. In addition to known sncRNAs, we identified numerous somatic piRNA-like RNAs. This study confirms the expression of pilRNAs in somatic tissues and outlines their major characteristics.

overall_design: ICC and Sm Int were collected from adult mice (C57BL/6). Small RNA was isolated from samples and cDNA libraries were generated for 454 sequencing. Sequences from FastA files were aligned to known sncRNA and the mouse mm9 genome. This was followed by subsequent novel small RNA annotation.

first: Grant

last: Hennig

first: Dickson

last: Luong

first: Bhupal

last: Bhetwal

first: Seungil

last: Ro

first: John

last: McCarrey

first: Wei

last: Yan


title: Tight coordination of protein translation and heat shock factor 1 activation supports the anabolic malignant state [ChIP-Seq]

first: Marc

last: Mendillo

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: A unifying characteristic of aggressive cancers is a profound anabolic shift in metabolism to enable sustained proliferation and biomass expansion.  The ribosome is centrally situated to sense metabolic states but whether it impacts systems that promote cellular survival is unknown.   Here, through integrated chemical-genetic analyses, we find that a dominant transcriptional effect of blocking protein translation in cancer cells is complete inactivation of heat shock factor 1 (HSF1), a multifaceted transcriptional regulator of the heat-shock response and many other cellular processes essential for tumorigenesis.  Translational flux through the ribosome reshapes the transcriptional landscape and links the fundamental anabolic processes of protein production and energy metabolism with HSF1 activity.  Targeting this link deprives cancer cells of their energy and chaperone armamentarium thereby rendering the malignant phenotype unsustainable.

overall_design: We used ChIP-Seq to examine affect of rocaglates and cycloheximide on HSF1 genomic occupancy in MCF7 and M0-91 cancer cells.

first: Sandro

last: Santagata

first: Yun-chi

last: Tang

first: Aravind

last: Subramanian

first: Casey

last: Perley

first: Stéphane

last: Roche

first: Bang

last: Wong

first: Rajiv

last: Narayan

first: Hyoungtae

last: Kwon

first: Martina

last: Koeva

first: Angelika

last: Amon

first: Todd

middle: R

last: Golub

middle: A

last: Porco

first: Luke

last: Whitesell

first: Susan

last: Lindquist


title: Depletion of stromal cells expressing fibroblast activation protein-α from skeletal muscle and bone marrow results in cachexia and anemia

first: Andrew

last: Deonarine

address: Hills Road

institute: Laboratory of Molecular Biology

summary: Fibroblast activation protein-α (FAP) identifies stromal cells of mesenchymal origin in human cancers and chronic inflammatory lesions. In mouse models of cancer, they have been shown to be immune suppressive, but studies of their occurrence and function in normal tissues have been limited. With a transgenic mouse line permitting the bioluminescent imaging of FAP(+) cells, we find that they reside in most tissues of the adult mouse. FAP(+) cells from three sites, skeletal muscle, adipose tissue, and pancreas, have highly similar transcriptomes, suggesting a shared lineage. FAP(+) cells of skeletal muscle are the major local source of follistatin, and in bone marrow they express Cxcl12 and KitL. Experimental ablation of these cells causes loss of muscle mass and a reduction of B-lymphopoiesis and erythropoiesis, revealing their essential functions in maintaining normal muscle mass and hematopoiesis, respectively. Remarkably, these cells are altered at these sites in transplantable and spontaneous mouse models of cancer-induced cachexia and anemia. Thus, the FAP(+) stromal cell may have roles in two adverse consequences of cancer: their acquisition by tumors may cause failure of immunosurveillance, and their alteration in normal tissues contributes to the paraneoplastic syndromes of cachexia and anemia.

overall_design: FAP+ cells were sorted from two mesenchymal tissues, visceral adipose and skeletal muscle, and from an epithelial organ, the pancreas. These were compared to MEFs. Cells were isolated in duplicate experiments and these were analysed separately. These were compared to previously published publically available CD4+ T-cell subset data.

first: E

middle: W

last: Roberts

first: A

first: J

middle: O

last: Jones

middle: E

last: Denton

first: C

last: Feig

first: S

last: Lyons

first: M

last: Espeli

last: Kraman

first: B

last: McKenna

first: R

last: Wells

first: Q

last: Zhao

first: O

last: Caballero

last: Larder

last: Coll

last: O'Rahilly

first: K

last: Brindle

last: Teichmann

first: D

last: Tuveson

middle: T

last: Fearon


title: Transcriptomes of K562 cell line

first: yadong

last: yang

address: No.1-104 Beichen West Road, Chaoyang

institute: Beijing Institute of Genomics

summary: To investigate the expression level of genes in K562 cells

overall_design: Profiling the transcriptome of K562

first: Songnian

last: Hu

first: Xiangdong

last: Fang


title: Proteomic and transcriptomic responses to thiamethoxam in the Sweetpotato whitefly, Bemisia tabaci (Hemiptera: Aleyrodidae)

first: Nina

last: Yang

state: Beijing

address: 12 Zhongguancun Nandajie, Haidian District

institute: Chinese Academy of Agricultural Sciences

summary: We investigated the transcriptional response to thiamethoxam in the Bemisia tabaci using Illumina sequencing technology. A total of 1,338 genes were differently expressed in the  thiamethoxam-resistant whiteflies.

overall_design: All the B biotype whiteflies were maintained on cabbage. The susceptible strain (TH-S) was cultured without exposure to any chemical insecticides. Before the sample collected, almost 10,000 thiamethoxam-resistant adult whiteflies were treated with 2,000 mg/L thiamethoxam (~LC80) to eliminate the heterozygous individuals. Then the survivors were collected after 48 hours and designated as the TH-2000 sample.  Then approximately 1,500 adult TH-S and TH-2000 were collected, respectively, The RNA was extracted and sequenced using Illumina HiSeq 2000.

first: Wen

last: Xie

first: Xin

first: Xuguo

last: Zhou

first: Youjun

last: Zhang


title: Defining the microglia transcriptome during disease progression in ALS transgenic mice

city: New York

first: Sean

last: O'Keeffe

address: 701 West 168th Street

institute: Columbia University

summary:
Purpose:  We purified spinal cord microglia utilizing percoll gradients and magnetic beads, followed by transcriptome profiling (RNA-seq) to define microglia expression profiles against other neural, immune cell-types.  We next observed how the microglai transcriptomes change during activation in the SOD1-G93A mouse model of motor neuron degeneration at 3 timepoints.  We also compared these profiles with that induced by LPS injection.
Results and conclusions:  ALS microglia were found to differ substantially from those activated by LPS and from M1/M2 macrophages by comparison with published datasets. These ALS microglia showing substantial induction of a "neurodegeneration-tailored phenotype", with induction of lysosomal, RNA splicing, and Alzheimer's disease pathway genes.  Overall they express a mixture of neuroprotective and neurotoxic factors during activation in ALS mice, showing that neuro-immune activation in the spinal cord is a double-edged sword.  We also detected the transcriptional nature of surface marker expression in microglia (CD11b, CD86, CD11c), and substantial T-cell microglia cross-talk using correlative microglia transcriptome/FACS analysis.

overall_design: 42 total RNA samples from purified spinal cord microglia were subjected to paired-end RNA-sequencing.  Parallel flow cytometry data was collected from the same spinal cords.

first: Isaac

last: Chiu

first: Tom

last: Maniatis


title: Synergistic interactions between CLAMP and MSL complex facilitate Drosophila dosage compensation

city: Providence

first: Erica

last: Larschan

address: 185 Meeting St.

institute: Brown University

summary: ChIP-seq and mRNA-seq experiments were performed to understand the role of the CLAMP protein in dosage compensation

overall_design: ChIP-seq experiments compared the binding profiles of CLAMP in male and female cells and mRNA-seq data to define the role of CLAMP in regulating genes on the X-chromosome

first: Eric

last: Bishop


title: Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos

status: Public on Jul 13 2013

first: Luis

middle: Alberto

last: Barrera

address: 77 Avenue Louis Pasteur

institute: Harvard University

summary: Understanding transcriptional regulatory networks requires the identification and characterization of cis-regulatory modules (CRMs), DNA sequences which can direct expression of associated genes to a specific cell type and/or developmental stage.  Reporter assays for the capacity of a candidate CRM to activate a heterologous promoter have been productive but suffer limited throughput or fail to convey information on cell type specificity.  We have developed an assay in which reporter constructs containing a pool of candidate CRMs are introduced in parallel to Drosophila embryos along with a common cell-type-specific second marker; candidate CRMs isolated by PCR from FACS-purified double-positive cells can by quantitated by high-throughput sequencing, and their relative abundance compared to those in the input cell population to detect activity in the cell type (or types) of interest.

overall_design: twi-CD2+/GFP+ cells in triplicate, and input (twi-CD2+) cells in triplicate for comparison; twi-CD2-/GFP+ cells in triplicate, and input (twi-CD2-) cells in triplicate for comparison; mef2-CD2+/GFP+ cells (single sample), and input (mef2-CD2-) cells in quintuplicate for comparison and variance estimation; mef2-CD2-/GFP+ cells in triplicate, and input (mef2-CD2-) cells in triplicate for comparison; duf:CD2+/GFP+ cells (single sample), and input (duf:CD2-) cells in quintuplicate for comparison and variance estimation; duf:CD2-/GFP+ cells in sextuplicate, and input (duf:CD2-) cells in sextuplicate for comparison.

first: Stephen

middle: S

last: Gisselbrecht

first: Martin

last: Porsch

first: Preston

last: Estep

first: Anastasia

last: Vedenko

first: Anton

last: Aboukhalil

first: Alexandre

last: Palagi

first: Yongsok

last: Kim

first: Xianmin

last: Zhu

first: Brian

last: Busser

first: Alan

last: Michelson

first: Martha

middle: L

last: Bulyk


title: Expression from Escherichia coli

status: Public on Jul 12 2013

city: Leuven

first: Kristof

last: Engelen

address: Kasteelpark Arenberg 20

institute: KULeuven

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

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Refer to individual Series


title: Escherichia coli RNA-Seq

summary: The goal of this study is to compare gene expression data for a well known model organism (Escherichia coli) using different technologies (NGS here,  microarray from GSE48776).

platform_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: mRNA profiles of Wild Type and two Mutant Strains (ydcR (b1439) MUTANT and yjiR (b4340) MUTANT), growth in minimal medium, were generated by deep sequencing, in triplicate, using Illumina MiSeq.


title: Decoding the transcriptional program of epidermal cell morphogenesis

first: Rebecca

middle: Fran

last: Spokony

address: 17 Lexington Avenue

department: Natural Sciences

institute: Baruch College

summary: Developmental programs are implemented by regulatory interactions between Transcription Factors (TFs) and their target genes, which remain yet poorly understood. While recent studies have focused on regulatory cascades of TFs that govern early development, little is known on how these are selected and controlled the ultimate cellular effectors of terminal differentiation. We addressed this question during late Drosophila embryogenesis when the finely tuned expression of a TF, Ovo/Shavenbaby (Svb), triggers the morphological differentiation of epidermal trichomes. We used chromatin immunoprecipitation and microarray profiling to identify Svb downstream target genes and show that Svb directly regulates a large set of terminal effectors of trichome formation. Functional assays delineated 18 Svb bound sequences driving specific expression of trichome effectors, with highly similar pattern and dynamics. Coupling computational modeling to functional dissection, we further investigated the regulatory logic of these enhancers. We find that these “terminal” enhancers harbor remarkable features with respect to their functional architectures. Trichome enhancers display weak if any clustering of Svb binding sites. Moreover, the in vivo function of each site relies on its intimate context, with a critical importance of the nucleotides flanking Svb binding sites. Finally, we identify additional cis-regulatory motifs, showing a broad diversity of positioning among trichome enhancers, and that critically contribute to their activity. Taken together, these results show that trichome formation is underpinned by unexpectedly diverse modes of regulation, and shed light on the functional architecture of enhancers governing a terminal differentiation program.

overall_design: Chromatin from 12-14 hour old embryos expressing svb tagged with GFP (Kondo T, Plaza S, Zanet J, Benrabah E, Valenti P, Hashimoto Y, Kobayashi S, Payre F, Kageyama Y: Small peptides switch the transcriptional activity of Shavenbaby during Drosophila embryogenesis. Science 2010, 329:336-339) was collected in duplicate.  Chromatin was immunoprecipitated using an antiGFP antibody and input chromatin was used as a control.

first: Kevin

last: White


title: The metabolic niche of a prominent sulfate-reducing human gut bacterium

city: St Louis

first: Federico

last: Rey

address: 4444 Forest Park Blvd

department: Pathology

institute: Washington University


title: Evaluating the Impact of Sequencing Depth on Transcriptome Profiling in Human Adipose

city: Philadelphia

first: Yichuan

last: Liu

address: 423 Guardian Drive

institute: University of Pennsylvania

summary: Recent advances in RNA sequencing (RNA-Seq) have enabled the discovery of novel transcriptomic variations that are not possible with traditional microarray-based methods. Tissue and cell specific transcriptome changes during pathophysiological stress, in disease cases versus controls and in response to therapies are of particular interest to investigators studying cardiometabolic diseases. Thus, knowledge on the relationships between sequencing depth and detection of transcriptomic variation is needed for designing RNA-Seq experiments and for interpreting results of analyses. Using deeply sequenced RNA-Seq data derived from adipose of a healthy individual before and after systemic administration of endotoxin (LPS), we investigated the sequencing depths needed for studies of gene expression and alternative splicing (AS). We found that to detect expressed genes and AS events, ~100 million (M) filtered reads were needed. However, the requirement on sequencing depth for the detection of LPS modulated differential expression (DE) and differential alternative splicing (DAS) was much higher. To detect 80% of events, ~300M filtered reads were needed for DE analysis whereas at least 400M filtered reads were necessary for detecting DAS. Although the majority of expressed genes and AS events can be detected with modest sequencing depths (~100M filtered reads), the estimated gene expression levels and exon/intron inclusion levels were less accurate. We report the first study that evaluates the relationship between RNA-Seq depth and the ability to detect DE and DAS in human adipose. Our results suggest that a much higher sequencing depth is needed to reliably identify DAS events than for DE genes.

overall_design: Random sampling the RNA-seq data in different depth for gene and alternative-splicing analysis

first: Jane

last: Ferguson

first: Chenyi

last: Xue

first: Ian

last: Silverman

last: Gregory

first: Muredach

last: Reilly

first: Mingyao

last: Li


title: Whole-genome bisulfite sequencing of two distinct interconvertible DNA methylomes of mouse embryonic stem cells

city: Nijmegen

first: Hendrik

last: Marks

address: Geert Grooteplein 26/28

department: Molecular Biology

institute: Radboud University Nijmegen, RIMLS

summary: This study describes the DNA methylation profiling using whole-genome bisulfite sequencing of mouse ES cells, either derived and maintained in 2i serum-free NDiff medium, or in the presence of serum and LIF, or maintained and derived in the presence of serum and LIF and subsequently adapted to 2i serum-free NDiff medium, or maintained and derived in the presence of 2i and LIF and subsequently adapted to 2i serum.

overall_design: DNA methylation profiling using whole-genome bisulfite sequencing of 14 samples, 3 different lines (E14, XT67E1, Rex/GFP-2i)  of pluripotent mouse ES cells as well during conversion from 2i to serum and vice versa.

first: Ehsan

last: Habibi

first: Arie

last: Brinkman

first: Julia

last: Arand

first: Leonie

middle: I

last: Kroeze

first: Hindrik

last: Kerstens

first: Filomena

last: Matarese

first: Konstantin

last: Lepikhov

first: Marta

last: Gut

first: Isabelle

last: Brun-Heath

first: Nina

middle: C

last: Hubner

first: Rosaria

last: Benedetti

first: Lucia

last: Altucci

first: Joop

last: Jansen

first: Jorn

last: Walter

first: Ivo

middle: G

last: Stunnenberg


title: Snyder_NFYA-1_GFP_L3

status: Public on Jul 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_4809
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
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: OP404(official name : OP404 genotype : unc-119(ed3) III; wgIs404(nfya-1::TY1-GFP-3xFLA; unc-119(+)) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden description : using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The NFYA-1::EGFP fusion protein is expressed in the correct nfya-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NFYA-1 transcription factor. made_by : Unknown ); Developmental Stage: L3; Genotype: unc-119(ed3) III; wgIs404(nfya-1::TY1-GFP-3xFLA; unc-119(+)); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L3; Target gene nfya-1; Strain OP404(official name : OP404 genotype : unc-119(ed3) III; wgIs404(nfya-1::TY1-GFP-3xFLA; unc-119(+)) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden description : using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The NFYA-1::EGFP fusion protein is expressed in the correct nfya-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NFYA-1 transcription factor. made_by : Unknown ); temp (temperature) 20 degree celsius

first: Mei

last: Zhong

first: Mike

last: Snyder

first: Cindie

last: Slightam

first: Stuart

last: Kim

first: John

last: Murray

first: Robert

last: Waterston

first: Mark

last: Gerstein

first: Wei

last: Niu

first: Judi

last: Janette

first: Debasish

last: Raha

first: Ashish

last: Agarwal

first: Valerie

last: Reinke

first: Mihail

last: Sarov

first: Anthony

last: Hyman


title: Snyder_NFYA-1_GFP_LateEMB

summary:
modENCODE_submission_4810
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
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: OP404(official name : OP404 genotype : unc-119(ed3) III; wgIs404(nfya-1::TY1-GFP-3xFLA; unc-119(+)) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden description : using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The NFYA-1::EGFP fusion protein is expressed in the correct nfya-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NFYA-1 transcription factor. made_by : Unknown ); Developmental Stage: Late Embryo; Genotype: unc-119(ed3) III; wgIs404(nfya-1::TY1-GFP-3xFLA; unc-119(+)); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage Late Embryo; Target gene nfya-1; Strain OP404(official name : OP404 genotype : unc-119(ed3) III; wgIs404(nfya-1::TY1-GFP-3xFLA; unc-119(+)) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden description : using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The NFYA-1::EGFP fusion protein is expressed in the correct nfya-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NFYA-1 transcription factor. made_by : Unknown ); temp (temperature) 20 degree celsius


title: Snyder_NFYA-1_GFP_YA

summary:
modENCODE_submission_4811
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
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: OP404(official name : OP404 genotype : unc-119(ed3) III; wgIs404(nfya-1::TY1-GFP-3xFLA; unc-119(+)) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden description : using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The NFYA-1::EGFP fusion protein is expressed in the correct nfya-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NFYA-1 transcription factor. made_by : Unknown ); Developmental Stage: Young adult; Genotype: unc-119(ed3) III; wgIs404(nfya-1::TY1-GFP-3xFLA; unc-119(+)); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage Young adult; Target gene nfya-1; Strain OP404(official name : OP404 genotype : unc-119(ed3) III; wgIs404(nfya-1::TY1-GFP-3xFLA; unc-119(+)) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden description : using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The NFYA-1::EGFP fusion protein is expressed in the correct nfya-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NFYA-1 transcription factor. made_by : Unknown ); temp (temperature) 20 degree celsius


title: Snyder_MED-1_GFP_MIDEMB

summary:
modENCODE_submission_4808
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
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: OP391(official name : OP391 genotype : unc-119(ed3) III; wgIs391(med-1::TY1 EGFP FLAG C; unc-119(+)) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden description : using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The MED-1::EGFP fusion protein is expressed in the correct med-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the MED-1 transcription factor. made_by : Unknown ); Developmental Stage: embryo; Genotype: unc-119(ed3) III; wgIs391(med-1::TY1 EGFP FLAG C; unc-119(+)); Sex: mixed Male and Hermaphrodite population;  EXPERIMENTAL FACTORS: Developmental Stage embryo; Target gene med-1; Strain OP391(official name : OP391 genotype : unc-119(ed3) III; wgIs391(med-1::TY1 EGFP FLAG C; unc-119(+)) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden description : using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The MED-1::EGFP fusion protein is expressed in the correct med-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the MED-1 transcription factor. made_by : Unknown ); temp (temperature) 20 degree celsius


title: Snyder_DVE-1_GFP_LateEMB

summary:
modENCODE_submission_4804
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
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: OP398(official name : OP398 genotype : unc-119(ed3) III; wgIs398(dve-1::TY1EGFPFLAG C;unc-119(+)) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden description : using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The DVE-1::EGFP fusion protein is expressed in the correct dve-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the DVE-1 transcription factor. made_by : Unknown ); Developmental Stage: Late Embryo; Genotype: unc-119(ed3) III; wgIs398(dve-1::TY1EGFPFLAG C;unc-119(+)); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage Late Embryo; Target gene dve-1; Strain OP398(official name : OP398 genotype : unc-119(ed3) III; wgIs398(dve-1::TY1EGFPFLAG C;unc-119(+)) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden description : using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The DVE-1::EGFP fusion protein is expressed in the correct dve-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the DVE-1 transcription factor. made_by : Unknown ); temp (temperature) 20 degree celsius


title: Snyder_HLH-30_GFP_L4

summary:
modENCODE_submission_4806
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
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: OP433(official name : OP433 genotype : unc-119(ed3) III; wgIs433(hlh-30::TY1 EGFP FLAG; unc-119(+)) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden description : using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The HLH-30::EGFP fusion protein is expressed in the correct hlh-30 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the HLH-30 transcription factor. made_by : Unknown ); Developmental Stage: L4; Genotype: unc-119(ed3) III; wgIs433(hlh-30::TY1 EGFP FLAG; unc-119(+)); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L4; Target gene hlh-30; Strain OP433(official name : OP433 genotype : unc-119(ed3) III; wgIs433(hlh-30::TY1 EGFP FLAG; unc-119(+)) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden description : using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The HLH-30::EGFP fusion protein is expressed in the correct hlh-30 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the HLH-30 transcription factor. made_by : Unknown ); temp (temperature) 20 degree celsius


title: seq-ab12181_H3K9acS10_873968_N2_L3

status: Public on Jul 26 2013

summary:
modENCODE_submission_5988
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: L3 Larva; Genotype: wild type; Sex: mixed Male and Hermaphrodite population;  EXPERIMENTAL FACTORS: Developmental Stage L3 Larva; temp (temperature) 20 degree celsius; Strain N2; Antibody ab12181-H3K9acS10ph-873968 (target is H3K9acS10ph)

first: Julie

last: Ahringer

first: Isabel

last: Latorre

first: Anne

last: Canonge


title: Snyder_DVE-1_GFP_L4

first: DCC

last: modENCODE

summary:
modENCODE_submission_4803
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
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: OP398(official name : OP398 genotype : unc-119(ed3) III; wgIs398(dve-1::TY1EGFPFLAG C;unc-119(+)) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden description : using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The DVE-1::EGFP fusion protein is expressed in the correct dve-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the DVE-1 transcription factor. made_by : Unknown ); Developmental Stage: L4; Genotype: unc-119(ed3) III; wgIs398(dve-1::TY1EGFPFLAG C;unc-119(+)); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L4; Target gene dve-1; Strain OP398(official name : OP398 genotype : unc-119(ed3) III; wgIs398(dve-1::TY1EGFPFLAG C;unc-119(+)) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden description : using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The DVE-1::EGFP fusion protein is expressed in the correct dve-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the DVE-1 transcription factor. made_by : Unknown ); temp (temperature) 20 degree celsius

first: Mei

last: Zhong


title: Snyder_F23B12.7_GFP_YA

summary:
modENCODE_submission_4805
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
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: OP429(official name : OP429 genotype : unc-119(ed3) III; wgIs429(F23B12.7::TY1GFP-3xFLA; unc-119(+)) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden description : using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The F23B12.7::EGFP fusion protein is expressed in the correct F23B12.7 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the F23B12.7 transcription factor. made_by : Unknown ); Developmental Stage: Young adult; Genotype: unc-119(ed3) III; wgIs429(F23B12.7::TY1GFP-3xFLA; unc-119(+)); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage Young adult; Target gene F23B12.7; Strain OP429(official name : OP429 genotype : unc-119(ed3) III; wgIs429(F23B12.7::TY1GFP-3xFLA; unc-119(+)) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden description : using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The F23B12.7::EGFP fusion protein is expressed in the correct F23B12.7 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the F23B12.7 transcription factor. made_by : Unknown ); temp (temperature) 20 degree celsius

first: Mike

last: Snyder

first: Cindie

last: Slightam