title: FoxA1 binding in asynchronous and mitotic HUH7 cells

first: Kenneth

middle: S.

last: Zaret

address: 9-132, SCTR, 3400 Civic Center Boulevard

department: Cell and Developmental Biology

institute: University of Pennsylvania School of Medicine

summary: During mitosis, RNA polymerase and most transcription factors are excluded from the chromosomes and transcription ceases.  The transcriptional re-activation of the genome, following mitosis, requires the re-setting of cell-type specific programs that were initially established during development.  However, only about one-fifth of transcription factors are retained on chromosomes throughout mitosis and a subset of these have been shown to facilitate target gene reactivation during mitotic exit.  How such “bookmarking” factors bind to chromatin in mitosis and re-activate transcription is central to the stability of transcriptional programs across multiple cell cycles.  We compared a diverse set of transcription factors involved in liver differentiation and found different modes of mitotic chromosome binding.  The pioneer transcription factor FoxA1, which is among the first to bind liver genes in development, exhibits virtually complete mitotic chromosome binding, whereas other liver factors bind with a range of efficiencies.  Yet genome-wide analysis shows that only about 15% of the FoxA1 interphase target sites are bound in mitosis; the latter include sites at genes for maintaining cell differentiation.  FoxA1 mutants that perturb specific and nonspecific DNA binding reveal a significant contribution of nonspecific binding events in mitotic chromatin.  Such nonspecific binding appears to spread from interphase FoxA1 targets and may serve as storage sites.  The hierarchy of specific binding, nonspecific binding, partial chromatin binding, and failure to bind mitotic chromosomes reflects the temporal sequence of the factors’ developmental roles in gene activation.

overall_design: Three replicate chIP-seq data sets each are included for mitotic and asynchronously cycling cells; a single input lane from each condition is also included.

first: Juan

last: Caravaca

first: Greg

first: Justin

last: Becker


title: mSWI/SNF (BAF) Complexes Facilitate Decatentation of DNA by Topoisomerase IIa

status: Public on Mar 30 2013

city: West Lafayette

first: Emily

last: Dykhuizen

state: IN

address: 201 S. University

department: medicinal chemistry and molecular pharmacology

country: USA

institute: Purdue University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Recent exon sequencing studies of human tumors have revealed that subunits of mSWI/SNF or BAF complexes are mutated in more than 20% of human malignancies, yet the mechanisms involved in tumor suppression is unclear. BAF chromatin remodeling complexes are polymorphic assemblies that use energy provided by ATP hydrolysis to regulate transcription through the control of chromatin structure and the placement of Polycomb (PcG) across the genome. Several proteins dedicated to this large multi-subunit complex, including SMARCA4 (BRG1) and BAF250A (ARID1A), are mutated at frequencies similar to that of many recognized tumor suppressors. In particular, the core ATPase BRG1 is mutated in 5-10% of childhood medulloblastoma (MB) and greater than 15% of Burkitt's Lymphoma (BL). Here we find a novel function of BAF complexes in decatenating newly replicated sister chromatids, which is necessary for proper chromosome segregation during mitosis. We find that deletion of Brg1, as well as the expression of Brg1 point mutants identified in human tumors leads to anaphase bridge formation (sister chromatids linked by catenated strands of DNA), and a G2/M phase block characteristic of the decatenation checkpoint. Endogenous BAF complexes directly interact with endogenous TopoIIα through BAF250a and are required for TopoIIα binding to about 12,000 sites over the genome. Our results indicate that TopoIIα’s chromatin binding is dependent on the ATPase activity of Brg1, which is compromised in oncogenic Brg1 mutants. These studies indicate that the ability of TopoIIα to prevent DNA entanglement at mitosis requires BAF complexes and suggest that this activity contributes to the role of BAF subunits as tumor suppressors.

overall_design: Examination of sites of TopoIIa activity in WT and Brg1-/- ES cells as defined by TopoIIa-DNA covalent adducts formed in the presence of etoposide

first: Gerald

middle: R

last: Crabtree


title: Transcriptomic analysis of Alishewanella species utilizing pectin as a sole carbon source

status: Public on Mar 29 2013

city: Seoul

first: Jaejoon

last: Jung

address: Anam-dong 5 Ga

country: South Korea

institute: Korea University

type: Expression profiling by high throughput sequencing

summary: Comparative transcriptomic analysis of three Alishewanella species utilizing pectin as a sole carbon source

sample_organism:
Alishewanella aestuarii
Alishewanella jeotgali
Alishewanella agri

overall_design: Gene expression level of three Alishewanella species grown on pectin was investigated and compared with A. jeotgali grown on succinate

first: Woojun

last: Park


title: miRNAs associated with the different human Argonaute proteins

city: Munich

first: Anne

last: Dueck

state: Bavaria

address: Biedersteiner Str.29

department: Institute of Pharmacology and Toxicology

country: Germany

institute: TUM

type: Non-coding RNA profiling by high throughput sequencing

summary: microRNAs (miRNAs) are small non-coding RNAs that function in literally all cellular processes. miRNAs interact with Argonaute (Ago) proteins and guide them to specific target sites located in the 3’ untranslated region (UTR) of target mRNAs leading to translational repression and deadenylation-induced mRNA degradation. Most miRNAs are processed from hairpin-structured precursors by the consecutive action of the RNase III enzymes Drosha and Dicer. However, processing of miR-451 is Dicer-independent and cleavage is mediated by the endonuclease Ago2. Here we have characterized miR-451 sequence and structure requirements for processing as well as sorting of miRNAs into different Ago proteins. Pre-miR-451 appears to be optimized for Ago2 cleavage and changes result in reduced processing. In addition, we show that the mature miR-451 only associates with Ago2 suggesting that mature miRNAs are not exchanged between different members of the Ago protein family. Based on cloning and deep sequencing of endogenous miRNAs associated with Ago1-3, we do not find evidence for miRNA sorting in human cells. However, Ago identity appears to influence the length of some miRNAs, while others remain unaffected.

overall_design: Examination of miRNAs associated with endogenous human Ago1-4 in HeLa cells

first: Christian

last: Ziegler

first: Alexander

last: Eichner

first: Eugene

last: Berezikov

first: Gunter

last: Meister


title: Genome wide mapping of histone 3 lysine 79 dimethylation in MLL rearranged and control human leukemia cell lines

status: Public on Apr 03 2013

city: Boston

first: Amit

last: Sinha

state: MA

address: 44 Binney St

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

summary: We report the genome wide distribution of H3K79 dimethylation in the human MLL-AF6 rearranged cell line ML2 as well as the human MOLM13 and HL60 cell lines

overall_design: Examination of H3K79 dimethylation in  the MLL-AF6 fusion positive human leukemia cell line ML2 and control cell lines MOLM-13 and HL60. The MLL-AF6 positive ML2 cell line (obtained from DSMZ) and the cell lines HL60 and MOLM 13 were grown under standard conditions and 1 million cells were fixed/crosslinked and used for ChIP-seq with H3K79 dimethylation specific antibody Ab3594 (Abcam)

first: Aniruddha

last: Deshpande

first: Liying

last: Chen

first: Scott

last: Armstrong


title: Sequences Associated with Centromere Competency in the Human Genome

city: Durham

first: Karen

middle: Elizabeth

last: Hayden

state: NC

address: 101 Science Drive

department: Institute for Genome Sciences and policy

institute: Duke University

summary: Centromeres, the sites of spindle attachment during mitosis and meiosis, are located in specific positions in the human genome, normally coincident with diverse subsets of alpha satellite DNA. While there is strong evidence supporting the association of some subfamilies of alpha satellite with centromere function, the basis for establishing whether a given alpha satellite sequence is or is not designated a functional centromere is unknown, and attempts to understand the role of particular sequence features in establishing centromere identity have been limited by the near identity and repetitive nature of satellite sequences. Utilizing a broadly applicable experimental approach to test sequence competency for centromere specification, we have carried out a genomic and epigenetic functional analysis of endogenous human centromere sequences available in the current human genome assembly. The data support a model in which functionally competent sequences confer an opportunity for centromere specification, integrating genomic and epigenetic signals and promoting the concept of context-dependent centromere inheritance.

overall_design: Sequences bound to CENP-A in HuRef cell line

middle: E

first: Erin

middle: D

last: Strome

first: Stephanie

last: Merret

first: Hye-Ran

last: Lee

first: Katharine

middle: M

last: Rudd

first: Huntington

middle: F

last: Willard


title: Characterization and detection of novel and conserved miRNAs in Potato

status: Public on Apr 01 2013

city: Dundee

first: Runxuan

last: Zhang

state: Angus

address: Errol Road, Invergowrie

department: Information and Computational Sciences

country: United Kingdom

institute: The James Hutton Institute

summary: small RNA profile of Solanum tuberosum group Andigena

first: Csaba

last: Hornyik


title: Interleukin-27 treated human macrophages induce the expression of novel miRNAs which may mediate anti-viral properties

city: Frederick

first: Xiaojun

last: Hu

state: MD

address: 1050 Boyles St.

department: CSP

institute: SAIC_Frederick, INc

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

overall_design: Refer to individual Series


title: The landscape of RNA polymerase II transcription initiation in C. elegans reveals a novel regulatory architecture

city: Cambridge

first: Thomas

middle: A

last: Down

address: Tennis Court Road

department: WT/CRUK Gurdon Institute

institute: University of Cambridge

summary: It has recently been shown that RNA Polymerase II transcription is far more extensive than previously thought, much of it not associated with protein-coding genes.  To investigate this phenomenon, we determined the genome-wide landscape of RNA Polymerase II transcription initiation and elongation in C. elegans.  We identify 73,500 distinct clusters of transcription initiation and find that initiation is often bidirectional. Strikingly, the majority of initiation events occur in regions with enhancer-like chromatin signatures. We also assign transcription initiation sites to 7691 protein coding genes, the majority previously unknown because of trans-splicing.

overall_design: Through mapping RNA PolII initiation (short capped RNAs) and elongation (long capped RNAs), we provide identification of transcription start sites.

first: Julie

last: Ahringer


title: Pbx and Prdm1a transcription factors differentially regulate subsets of the fast skeletal muscle program in zebrafish

status: Public on Mar 28 2013

city: Seattle

first: Stephen

last: Tapscott

state: WASHINGTON

address: 1100 Fairview N. Ave

department: Human Biology

institute: Fred Hutch Cancer Research Center

summary: The basic helix-loop-helix factor Myod initiates skeletal muscle differentiation by directly and sequentially activating sets of muscle differentiation genes, including those encoding muscle contractile proteins. We hypothesize that Pbx homeodomain proteins direct Myod to a subset of its transcriptional targets, in particular fast twitch muscle differentiation genes, thereby regulating the competence of muscle precursor cells to differentiate. We have previously shown that Pbx proteins bind with Myod on the promoter of the zebrafish fast muscle gene mylpfa and that Pbx proteins are required for Myod to activate mylpfa expression and the fast-twitch muscle-specific differentiation program in zebrafish embryos. Here we have investigated the interactions of Pbx with another muscle fiber-type regulator, Prdm1a, a SET-domain DNA-binding factor that directly represses mylpfa expression and fast muscle differentiation. The prdm1a mutant phenotype, early and increased fast muscle differentiation, is the opposite of the Pbx-null phenotype, delayed and reduced fast muscle differentiation. To determine whether Pbx and Prdm1a have opposing activities on a common set of genes, we used RNA-seq analysis to globally assess gene expression in zebrafish embryos with single- and double-losses-of-function for Pbx and Prdm1a. We find that the levels of expression of certain fast muscle genes are increased or approximately wild type in pbx2/4-MO;prdm1a-/- embryos, suggesting that Pbx activity normally counters the repressive action of Prdm1a for a subset of the fast muscle program. However, other fast muscle genes require Pbx but are not regulated by Prdm1a. Thus, our findings reveal that subsets of the fast muscle program are differentially regulated by Pbx and Prdm1a. Our findings provide an example of how Pbx homeodomain proteins act in a balance with other transcription factors to regulate subsets of a cellular differentiation program.

overall_design: Total RNA samples were genotyped and pooled for 4 sample types: control-MO;prdm1+/+; control-MO;prdm1-/-; pbx2/4-MO;prdm1+/+; and pbx2/4-MO;prdm1-/- embryos at the 10 somite (s) stage from three independent sets of egg collections/injections.

first: Lisa

last: Maves

first: Zizhen

last: Yao


title: Interleukin-27 treated human macrophages induce the expression of novel miRNAs which may mediate anti-viral properties (RNA-seq)

summary: In this study, we hypothesized that IL-27 could induce the expression of novel miRNAs in macrophages which may have functional relevance in terms of anti-viral activity. In this study, primary monocytes were differentiated into macrophages using M-CSF (M-Mac) or with a combination of M-CSF and IL-27 (I-Mac) for seven days. Following this, total RNA was extracted from these cells and deep sequencing was performed, in parallel with gene expression microarrays. Using the novel miRNA discovery software, miRDeep, seven novel miRNAs were discovered in the macrophages, four of which were expressed higher in I-Mac (miRNAs 2.1, 8.1, 9.1 and 14.2) whilst three were detected in both M-Mac and I-Mac (miRNAs 9.3, 13.6 and 15.8). The expression of six of the seven novel miRNAs was highly correlated with qRT-PCR using specific primer/probes designed for the novel miRNAs. Gene expression microarray further demonstrated that a number of genes were potentially targeted by these differentially expressed novel miRNAs.

overall_design: screening novel and known miRNAs which may have antiviral properties in 2 different treatments in 2 donors.

first: Sanjay

last: Swaminathan

first: Tomozumi

last: Imamichi

first: Dawei

last: Huang

first: Richard

last: Lempicki


title: Comparison of DNA methylation in human tissues

city: Davis

first: Janine

last: LaSalle

state: CA

address: Medical Microbiology and Immunology

institute: UC Davis

type: Methylation profiling by high throughput sequencing


title: The consequences of rapid mating system evolution in crucifer genomes

city: Toronto

last: Wright

state: Ontario

address: 25 Willcocks Street

department: Department of Ecology and Evolutionary Biology

country: Canada

institute: University of Toronto

summary: We compare RNA expression and polymorphism patterns between C. rubella and its outcrossing progenitor C. grandiflora. There is a clear shift in the expression of genes associated with flowering phenotypes; a similar shift is seen in the related genus Arabidopsis, where self-fertilization evolved about 1 million years ago.

sample_organism:
Capsella rubella
Capsella grandiflora

platform_organism:
Capsella rubella
Capsella grandiflora

overall_design: This is a two group comparison of gene expression between the self-compatible Capsella Rubella and out-crossing Capsella Grandiflora mixed stage flowerbuds.  Leaf expression is also provided as an annotation reference dataset.

first: Tanja

last: Slotte

first: Khaled

last: Hazzouri

first: J

last: Ågren

first: Daniel

last: Koenig

first: Florian

last: Maumus

first: Yalong

last: Guo

first: Kim

last: Steige

first: Adrian

last: Platts

first: Juan

middle: S

last: Escobar

first: L

middle: K

last: Newman

first: Wei

last: Wang

first: Terezie

last: Mandáková

first: Emilio

last: Vello

last: Smith

first: Joshua

last: Steffen

first: Shohei

last: Takuno

first: Yaniv

last: Brandvain

first: Graham

last: Coop

first: Peter

last: Andolfatto

first: Tina

middle: T

first: Mathieu

last: Blanchette

last: Clark

first: Hadi

last: Quesneville

first: Magnus

last: Nordborg

first: Brandon

last: Gaut

first: Martin

last: Lysak

first: Jerry

last: Jenkins

first: Jane

last: Grimwood

first: Jarrod

last: Chapman

first: Simon

last: Prochnick

first: Shengqiang

last: Shu

last: Rokhsar

first: Jeremy

last: Schmutz

first: Detlef

last: Weigel

middle: I


title: A dynamic H3K27ac signature defines VEGF-regulated endothelial enhancers

status: Public on Mar 31 2013

middle: J

last: Park

address: 10 Shattuck St

department: Center for Biomedical Informatics

institute: Harvard Medical School

summary: Histone modifications are now well-established regulators of transcriptional programs that distinguish distinct cell states. However, the kinetics of histone modification and their role in mediating rapid, signal-responsive changes in gene expression have been little studied on a genome-wide scale. Vascular endothelial growth factor A (VEGF), a major regulator of angiogenesis, rapidly triggers changes in transcriptional activity of human umbilical vein endothelial cells (HUVECs). Here we used chromatin immunoprecipitation and high throughput sequencing (ChIP-seq) to measure genome-wide changes in histone H3 acetylation at lysine 27 (H3K27ac), a marker of active enhancers {Kharchenko et al., 2011, Nature, 471, 480-5;Zentner et al., 2011, Genome Res, 21, 1273-83;Rada-Iglesias et al., 2011, Nature, 470, 279-83; Creyghton et al., 2010, Proc Natl Acad Sci U S A, 107, 21931-6 }, after 0, 1, 4, and 12 hours of VEGF stimulation. We show that sites with greatest H3K27ac changes were associated tightly with p300, a histone acetyltransferase. This dynamic H3K27ac signature defined transcriptional elements that are functionally linked to angiogenesis, participate in rapid VEGF-stimulated changes in chromatin conformation, and mediate VEGF-induced transcriptional responses. Dynamic H3K27ac deposition required p300 activity and did not involve altered nucleosome occupancy. Our results demonstrate that capture of dynamic changes in H3K27ac provides a new approach to define the activity of functional genomic elements and implicate epigenetic modifications in rapid signal-responsive transcriptional regulation.

overall_design: ChiP-seq timecourse of H3K27ac, ETS1, p300 chromatin occupancy, mRNA expression and DNA hypersensitivity of HUVEC cells stimulated with VEGF for 0, 1, 4, and 12 hours

first: Bing

last: Zhang

first: Daniel

last: Day

first: Joshua

last: Ho

first: Lingyun

last: Song

first: Jingjing

last: Cao

first: Gregory

last: Crawford

first: William

last: Pu


first: Janine

last: LaSalle

summary: As genome-scale DNA methylation sequencing technologies have improved it has become apparent that tissue-specific methylation can occur not only at promoters, enhancers, and CpG islands but also over larger genomic regions. In most human tissues, the vast majority of the genome is highly methylated (>70%). However, genomic sequencing of bisulfite-treated DNA (MethylC-seq) has revealed large partially methylated domains (PMDs) in some human cell lines. However, to date only cultured cells and some cancers have shown evidence for PMDs, suggesting that PMDs may not be observed in normal human tissues.  Here we performed MethylC-seq in a set of human tissues and found that full-term human placenta shows clear evidence of PMDs.

overall_design: Examination of four human tissue samples by MethylC-seq, with one tissue (placenta) having a technical replicate (taken from same placenta) and two additional biological replicates (from different placentas)

first: Diane

last: Schroeder


title: Evolution of the eye transcriptome under constant darkness in Sinocyclocheilus cavefish

city: Beijing

first: Fanwei

last: Meng

address: 1 Beichen West Road,Chaoyang District

department: State Key Laboratory of Biomembrane and Membrane Biotechnology

country: China

institute: Institue of Zoology, Chinese Academy of Sciences

summary: we report a transcriptome-wide comparative investigation between surface and cave species in Sinocyclocheilus. De novo transcriptome assemblies were performed on surface and cave species; then the Sinocyclocheilus contigs were annotated with Gene Ontology. RNA-Seq assays revealed reduced transcription of a series of visual phototransduction and retinal disease related genes in cave-dwelling species compared with surface species. Degeneration of the retina in Sinocyclocheilus cavefish might occur in a lens-independent way by the down-regulation of several transcriptional factors, which have direct roles in retina development and maintenance, such as crx, rorb and Wnt pathway members.

sample_organism:
Sinocyclocheilus angustiporus
Sinocyclocheilus anophthalmus

overall_design: Examination of 2 different eye samples in 2 Sinocyclocheilus species.

first: John

middle: H

last: Postlethwait


title: High-throughput transcriptome sequencing of an AML-M2 patient in two stages: primary tumor and remission.

city: Zhangzhou

first: AYang

last: Wu

address: 59, Shengli Road

institute: Zhangzhou municipal hospital of Fujian province

summary: In order to detect the transcriptomic differences during chemotherapy treatment of de novo AML, we adopted massively parallel pyrosequencing of mRNAs (RNA-seq) using blood tissues of an patient with AML (FAB subtype M2) in tumor stage and remission stage. We obtained a total of 34.6 and 30.8 million paired reads from the two samples. The RNA-seq data derived from the sample illustrated the differentially expression genes between the two stages.

overall_design: Blood samples of an AML-M2 patient in two stages examined: primary tumor and chemotherapy induced remission.

first: Wu

last: AYang


title: TALE transcription factors binding and transcriptional effect [ChIP-Seq]

city: Madrid

last: Mateos San Martín

address: Melchor Fernández Almagro 3

department: DBDC

country: Spain

institute: Fundación CNIC

summary: Meis, Prep and Pbx1 TALE homeoproteins interactions with Hox proteins are essential for development and disease. Although Meis and Prep behave similarly in vitro, their in vivo activities remain largely unexplored. We show that Prep and Meis interact with largely independent sets of genomic sites and select different DNA binding sequences, with Prep associating mostly with promoters and house-keeping genes and Meis with promoter-remote regions and developmental genes. Hox target sequences associate strongly with Meis but not with Prep binding sites, while Pbx1 cooperates with both Prep and Meis. Accordingly, Meis1 shows strong genetic interaction with Pbx1 but not with Prep1. Meis1 and Prep1 nonetheless co-regulate a subset of genes, predominantly through opposing effects. Notably, the TALE homeoprotein binding profile subdivides Hox clusters into two domains differentially regulated by Meis1 and Prep1. After duplication of the ancestral gene, Meis and Prep thus specialized their interactions but maintained significant regulatory coordination.

overall_design: ChIP-seq of 3 TALE proteins in E11.5 C57BL/6 embryonic mice


overall_design: Examination of gene expression in human placenta using RNA-seq, with one biological replicate (taken from same placenta)


title: Analysis of the Transcriptomes of Giardia intestinalis Assemblages A, B and E Using Strand-specific RNA-seq

city: Stockholm

first: Oscar

last: Franzen

address: Berzelius väg 35

department: Department of Cell and Molecular Biology

country: Sweden

institute: Karolinska Institutet

summary: We have performed strand-specific RNA-seq of trophozoites from four different Giardia intestinalis strains (A=WB and AS175, B=GS, E=P15).

overall_design: Comparison of mRNA levels in four different Giardia intestinalis strains.

first: Jon

last: Jerlstrom-Hultqvist

first: Johan

last: Ankarklev

first: Bjorn

last: Andersson

first: Staffan

last: Svard


title: Genome and transcriptome of the duck

city: shenzhen

first: wubin

last: qian

address: beishan road

institute: beijing genomics institute

summary: The reads of duck transcripome was mapped to the duck genome and help to identify the UTR regions of predicted genes. The expression level difference between the tissue spleen and liver will help us to detect the immune-related and fatty acid metabolism related genes.

overall_design: Duck transcriptome was sequenced to improve the gene annotation quality, and to detect the differently expressed genes in liver and spleen tissues.

first: Ning

last: Li

first: Yinhua

last: Huang


title: mRNA-Seq of brain tissue from honeybee (Apis mellifera) drones (male), workers (female) and queens (female).

status: Public on Mar 27 2013

city: Duesseldorf

first: Christina

last: Schulte

address: Universitaetssrasse 1

department: Evolutionary Genetics

institute: Heinrich-Heine-Universitaet

summary: Transcriptional profiling of brain tissue of was performed by RNA-SEQ in workers, queens and males. The sex and caste specific expressed and spliced genes were examined comparing drone, worker and queen honeybees.

overall_design: Examination of mRNA profiles in heads of male, worker and queen honeybees pupae were compared.

last: Vleurinck (née Schulte)

first: David

last: Sturgill

first: Martin

last: Beye


title: An Ancient Transcription Factor Initiates the Burst of piRNA Production During Early Meiosis in Mouse Testes (smallRNA-Seq)

city: Worcester

first: Christian

last: Roy

state: Massachusetts

address: 364 Plantation St

institute: Umass Med

summary: Animal germ cells produce PIWI-interacting RNAs (piRNAs), small silencing RNAs that suppress transposons and enable gamete maturation. Mammalian transposon-silencing piRNAs accumulate early in spermatogenesis, whereas pachytene piRNAs are produced later during post-natal spermatogenesis and account for >95% of all piRNAs in the adult mouse testis. Mutants defective for pachytene piRNA pathway proteins fail to produce mature sperm, but neither the piRNA precursor transcripts nor the trigger for pachytene piRNA production is known. Here, we show that the transcription factor A-MYB initiates pachytene piRNA production. A-MYB drives transcription of both pachytene piRNA precursor RNAs and the mRNAs for core piRNA biogenesis factors, including MIWI, the protein through which pachytene piRNAs function. A-MYB regulation of piRNA pathway proteins and piRNA genes creates a coherent feed-forward loop that ensures the robust accumulation of pachytene piRNAs. This regulatory circuit, which can be detected in rooster testes, likely predates the divergence of birds and mammals.

sample_organism:
Gallus gallus
Mus musculus

platform_organism:
Gallus gallus
Mus musculus

overall_design: smallRNA-Seq in mouse and rooster testes

first: Xin

middle: Z

first: Phillip

last: Zamore


title: RNA-seq analysis of Salmonella enterica Typhimurium LT2

status: Public on Mar 26 2013

city: Wellesley

first: Brian

last: Tjaden

address: 106 Central Street

institute: Wellesley College

summary: We performed whole-genome transcriptomic analyses of the Salmonella Typhimimurium genome during  glucose-phosphate stress.  In particular, we wanted to elucidate the role of the the small RNA SgrS and protein regulator SgrT in the stress response.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

overall_design: Wild-type Salmonella cells, mutants of Salmonella either lacking sgrS or  lacking SgrS RNA/ SgrT peptide function were subject to glucose-phoshate stress

first: Divya

last: Balasubramanian

first: Carin

last: Vanderpool


title: An Ancient Transcription Factor An Ancient Transcription Factor During Early Meiosis in Mouse Testes (PAS-Seq and CAGE)

overall_design: PAS-Seq and CAGE in mouse testes


title: Computational Analysis of Bacterial RNA-Seq Data

summary: RNA-seq analysis was carried out on N. gonorrhoeae grown in vitro to verify accuracy of a novel RNA-seq analysis program, Rockhopper

overall_design: Three replicates of N. gonorrhoeae grown in vitro

first: Ryan

last: McClure


title: RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655

summary: Expression profiles of wild-type and SgrR mutant E. coli strains under aMG and 2-DG-induced stress. Expression profiles of E. coli overexpressing SgrS sRNA.

overall_design: Illumina RNA-Seq of total RNA extracted from wild-type, SgrR/SgrS mutant and SgrS overexpressing E. coli strains grown in different conditions.

first: Maksym

last: Bobrovskyy

first: Yan

last: Sun

first: Gregory

last: Richards


title: DNA methylomes of the fire ant Solenopsis invicta.

city: Atlanta

first: Brendan

last: Hunt

state: GA

address: 310 Ferst Dr

department: School of Biology

institute: Georgia Institute of Technology

summary: We used whole bodies of four different adult fire ant morphs (alate queens, workers, haploid males, and diploid males) from a single polygyne colony to generate single-base resolution DNA methylation maps.

overall_design: DNA was extracted from whole bodies of individual males, individual queens, and pooled workers.  Bisulfite conversion and sequencing was performed by Beijing Genomics Institute (Shenzhen, China).  Unmethylated enterobacteria phage lambda  DNA (GenBank accession: J02459.1) was added to each genomic DNA sample as a control for bisulfite conversion efficiency.

middle: G

first: Karl

last: Glastad

first: Soojin

middle: V

last: Yi

first: Michael

last: Goodisman


title: Whole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis infection in vitro

city: Dublin

last: MacHugh

address: University College Dublin, Belfield

department: College of Agriculture, Food Science and Veterinary Medicine

country: Ireland

institute: University College Dublin

summary:
Background: Mycobacterium bovis, the causative agent of bovine tuberculosis, is an intracellular pathogen that can persist inside host macrophages during infection via a diverse range of mechanisms that subvert the host immune response. In the current study, we have analysed and compared the transcriptomes of M. bovis-infected monocyte-derived macrophages (MDM) purified from six Holstein-Friesian females with the transcriptomes of non-infected control MDM from the same animals over a 24 h period using strand-specific RNA sequencing (RNA-seq). In addition, we compare gene expression profiles generated using RNA-seq with those previously generated by us using the high-density Affymetrix® GeneChip® Bovine Genome Array platform from the same MDM-extracted RNA.
Results: A mean of 7.2 million reads from each MDM sample mapped uniquely and unambiguously to single Bos taurus reference genome locations. Analysis of these mapped reads showed 2,584 genes (1,392 upregulated; 1,192 downregulated) and 757 putative natural antisense transcripts (558 upregulated; 119 downregulated) that were differentially expressed based on sense and antisense strand data, respectively (adjusted P-value ≤ 0.05). Of the differentially expressed genes, 694 were common to both the sense and antisense data sets, with the direction of expression (i.e. up- or downregulation) positively correlated for 693 genes and negatively correlated for the remaining gene. Gene ontology analysis of the differentially expressed genes revealed an enrichment of immune, apoptotic and cell signalling genes. Notably, the number of differentially expressed genes identified from RNA-seq sense strand analysis was greater than the number of differentially expressed genes detected from microarray analysis (2,584 genes versus 2,015 genes). Furthermore, our data reveal a greater dynamic range in the detection and quantification of gene transcripts for RNA-seq compared to microarray technology.
Conclusions: This study highlights the value of RNA-seq in identifying novel immunomodulatory mechanisms that underlie host-mycobacterial pathogen interactions during infection, including possible complex post-transcriptional regulation of host gene expression involving antisense RNA.

overall_design: Description of the transcriptomic host response after infection of bovine monocyte-derived macrophages with Mycobacterium bovis

first: Nicolas

middle: C

last: Nalpas

first: Stephen

last: Park

last: Magee

first: Maria

last: Taraktsoglou

first: John

last: Browne

first: Kevin

last: Conlon

first: Kévin

last: Rue-Albrecht

first: Kate

last: Killick

first: Karsten

last: Hokamp

first: Amanda

last: Lohan

last: Loftus

first: Eamonn

last: Gormley

last: Gordon


title: An Ancient Transcription Factor Initiates the Burst of piRNA Production During Early Meiosis in Mouse Testes (ChIP-Seq)

first: Christian

last: Roy

overall_design: ChIP sequencing in mouse and rooster testes.

first: Xin

last: Li

first: Phillip

last: Zamore


title: An Ancient Transcription Factor Initiates the Burst of piRNA Production During Early Meiosis in Mouse Testes (RNA-Seq)

overall_design: Transcriptome and ChIP sequencing in mouse and rooster testes


title: Genome Wide Association identifies Novel Loci Involved Fungal Communication

city: Berkeley

first: Charles

middle: Robert

last: Hall

address: 341 Koshland Hall

department: Plant and Microbial Biology

institute: UC Berkeley

summary: Understanding how genomes encode complex cellular and organismal behaviors is an outstanding challenge of modern genetics.  Unlike classical screening methods, analysis of the genetic variation that occurs naturally in wild populations can enable rapid, genome-scale trait mapping with a medium-throughput experimental design.  Here we describe the results of the first genome-wide association analysis (GWAS) of a microbial eukaryote, using wild isolates of the filamentous fungus Neurospora crassa.  We transcriptionally profiled each of 112 individuals collected in Louisiana and used RNA-seq data to genotype each strain at thousands of genetic loci genome-wide. We used these genotypes in a mapping analysis of microbial communication. In N. crassa, germinated asexual spores (germlings) sense the presence of other germlings, grow toward them in a coordinated fashion, and fuse. We evaluated germlings of each strain for their ability to chemically sense, chemotropically seek, and undergo cell fusion. GWAS identified one gene, NCU04379 (cse-1, encoding a homolog of neuronal calcium sensor), at which inheritance was strongly associated with the efficiency of germling communication. Deletion of cse-1 significantly lowered germling communication and fusion, and two genes encoding predicted binding partners of CSE-1 were also required for the communication trait. Additionally, mining our association results for signaling and secretion genes with a potential role in germling communication, we validated six more novel determinants of germling communication, including a secreted protease and two other genes whose deletion conferred a novel phenotype of increased communication and multi-germling fusion. These results establish protein secretion as a linchpin of germling communication in N. crassa and shed light on the regulation of communication molecules in this fungus. Our study demonstrates the power of population-genetic analyses for the rapid identification of genes contributing to complex traits in microbial species.

overall_design: 112 mycelial mRNA profiles of 16 hour wild type (WT) Neurospora crassa strains were generated by deep sequencing, using Illumina GAIIx.

first: Javier

last: Palma-Guerrero

middle: R

first: David

last: Kowbel

first: Juliet

last: Welch

middle: W

last: Taylor

first: Rachel

middle: B

last: Brem

first: Louise

middle: N

last: Glass


title: Mapping Epigenomic Type-Specific Differences Occurring During Hematopoiesis [ChIP-Seq]

status: Public on Mar 25 2013

city: Memphis

first: Brian

last: Abraham

state: TN

address: 262 Danny Thomas Blvd

department: Computational Biology

institute: St. Jude Children's Research Hospital

summary: Formation of the blood from self-renewing hematopoietic stem cells to terminal lineages necessarily involves epigenomic modifications of the genome to control regulator and signature gene expression. By analysing the global expression profiles of hematopoietic stem cells (HSCs), in vivo differentiated CD4+ T cells and CD19+ B cells as well as in vitro differentiated erythrocyte precursor cells, we identified hundreds of transcripts showing type-specific expression in these cell types.  To understand the epigenomic changes related to tissue-specific expression during HSC differentiation, we examined the genome-wide distribution of H3K4me1, H3K4me3, H3K27me1, H3K27me3, histone variant H2A.Z, chromatin remodeler BRG1, and RNA Polymerase II in the same four cell types, as well as embryonic stem cells.  Analysis of these datasets revealed that numerous key differentiation genes are primed for expression by Brg1 and Pol II binding, as well as bivalent modifications in the HSCs prior to their expression in downstream differentiated cell types. Much of this bivalency in HSC is retained from embryonic stem cells.  After differentiation, these modified regions resolve to active chromatin modification configuration in the specific lineage, while in parallel differentiated lineages the bivalent modification remains; Pol II and Brg1 are lost in closer lineages but bivalency resolves to silent monovalency in more distant lineages. Correlation of tissue-specific gene expression with the epigenomic changes predicts tens of thousands of potential common enhancers and tissue-specific enhancers, which may critically contribute to the expression patterns. We provide a valuable dataset for further understanding the regulatory mechanisms of differentiation and function of blood lineages.

overall_design: ChIP-Seq: profiling of DNA-associated proteins in blood cell subsets.

first: Kairong

last: Cui

first: Qingsong

last: Tang

first: Keji

last: Zhao


title: An Ancient Transcription Factor Initiates the Burst of piRNA Production During Early Meiosis in Mouse Testes

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

overall_design: Refer to individual Series


title: Identifying host pathogenic pathways in bovine digital dermatitis by RNA-Seq analysis of lesions

city: Manchester

first: rachel

middle: anne

last: scholey

address: Oxford road

institute: University of Manchester

summary: Digital dermatitis is a painful foot disease compromising welfare in dairy cattle. The disease has a complex multibacterial aetiology, but little is known about its pathogenesis. In this study, gene expression in skin biopsies from five bovine digital dermatitis lesions and five healthy bovine feet was compared using RNA-Seq technology. Differential gene expression was determined after mapping transcripts to the Btau 4.0 genome. Pathway analysis identified gene networks involving differentially expressed transcripts. Bovine digital dermatitis lesions had increased expression of mRNA for a2-macroglobulin-like 1, a protein potentially involved in bacterial immune evasion and bacterial survival. There was increased expression of keratin 6A and interleukin 1b mRNA in bovine digital dermatitis lesions, but reduced expression of most other keratin and keratin-associated genes. There was little evidence of local immune reactions to the bacterial infection present in lesions.

overall_design: Ten samples were processed; five normal skin biopsies from the hind foot skin and five digital dermatitis lesions (large (>2cm) red raw in appearance).

first: R

last: Scholey


title: Mapping Epigenomic Type-Specific Differences Occurring During Hematopoiesis

summary:
Formation of the blood from self-renewing hematopoietic stem cells to terminal lineages necessarily involves epigenomic modifications of the genome to control regulator and signature gene expression. By analysing the global expression profiles of hematopoietic stem cells (HSCs), in vivo differentiated CD4+ T cells and CD19+ B cells as well as in vitro differentiated erythrocyte precursor cells, we identified hundreds of transcripts showing type-specific expression in these cell types.  To understand the epigenomic changes related to tissue-specific expression during HSC differentiation, we examined the genome-wide distribution of H3K4me1, H3K4me3, H3K27me1, H3K27me3, histone variant H2A.Z, chromatin remodeler BRG1, and RNA Polymerase II in the same four cell types, as well as embryonic stem cells.  Analysis of these datasets revealed that numerous key differentiation genes are primed for expression by Brg1 and Pol II binding, as well as bivalent modifications in the HSCs prior to their expression in downstream differentiated cell types. Much of this bivalency in HSC is retained from embryonic stem cells.  After differentiation, these modified regions resolve to active chromatin modification configuration in the specific lineage, while in parallel differentiated lineages the bivalent modification remains; Pol II and Brg1 are lost in closer lineages but bivalency resolves to silent monovalency in more distant lineages. Correlation of tissue-specific gene expression with the epigenomic changes predicts tens of thousands of potential common enhancers and tissue-specific enhancers, which may critically contribute to the expression patterns. We provide a valuable dataset for further understanding the regulatory mechanisms of differentiation and function of blood lineages.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series.


title: Comparative transcriptional profiling provides insights into the evolution and development of the zygomorphic flower of Vicia sativa (Papilionoideae)

city: Lanzhou

first: Zhipeng

last: Liu

address: No. 768, Jiayuguan west road

institute: College of Pastoral Agricultural Science and Technology, Lanzhou University

summary:
Background: Vicia sativa (the common vetch) possesses a predominant zygomorphic flower and belongs to the subfamily Papilionoideae, which is related to Arabidopsis thaliana in the eurosid II clade of the core eudicots. Each vetch flower consists of 21 concentrically arranged organs: the outermost five sepals, then five petals and ten stamens, and a single carpel in the center.
Methodology/Principal Findings: We explored the floral transcriptome to examine a genome-scale genetic model of the zygomorphic flower of vetch. mRNA was obtained from an equal mixture of six floral organs, leaves and roots. De novo assembly of the vetch transcriptome using Illumina paired-end technology produced 71,553 unigenes with an average length of 511 bp. We then compared the expression changes in the 71,553 unigenes in the eight independent organs through RNA-Seq Quantification analysis. We predominantly analyzed gene expression patterns specific to each floral organ and combinations of floral organs that corresponded to the traditional ABC model domains. Comparative analyses were performed in the floral transcriptomes of vetch and Arabidopsis, and genomes of vetch and Medicago truncatula.
Conclusions/Significance: Our comparative analysis of vetch and Arabidopsis showed that the vetch flowers conform to a strict ABC model. We analyzed the evolution and expression of the TCP gene family in vetch at a whole-genome level, and several unigenes specific to three different vetch petals, which might offer some clues toward elucidating the molecular mechanisms underlying floral zygomorphy. Our results provide the first insights into the genome-scale molecular regulatory network that controls the evolution and development of the zygomorphic flower in Papilionoideae.

overall_design: Examination of the transcriptomic changes in the six floral organs, leaves and roots in common vetch.

first: Zhibiao

first: Yanrong

last: Wang


title: Mapping Epigenomic Type-Specific Differences Occurring During Hematopoiesis [RNA-Seq]

overall_design:
RNA-Seq: This submission comprises RNA-Seq profiling of in vivo differentiated human B cells and hematopoietic stem cells.
Re-analyzed data for three cell types: The HSCs were previously uploaded as GSM651554 (SRX037948), but processed differently for this upload. The erythrocyte precursors and T cells have also been previously uploaded as GSM651555 (SRX037949) and GSM406414 (SRX005317), respectively.  They were treated as in GSM651554, but processed as here.  The processed files generated by our re-analysis are linked below as supplementary files.


title: Transcript structures in Shewanella sp W3-18-1

status: Public on Mar 21 2013

first: Wenjun

last: Shao

address: 2151 Berkeley Way

department: Molecular and Cell Biology

institute: University of California

summary: 5' RNASeq of mRNA from Shewanella sp W3-18-1 grown aerobically in Luria-Bertani broth (LB) and defined lactate minimal medium

overall_design: 5'-end mRNA profiles of mid-log phase bacterial cells growing in LB or lactate medium were generated by next-generation sequencing.

first: Morgan

last: Price

first: Adam

middle: M

last: Deutschbauer

middle: P

last: Arkin


title: Transcriptome-profiling (RNA-seq) and Ribosome-profiling (Ribo-seq) in proliferation, quiescence, senescence and transformed states.

status: Public on Mar 24 2013

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

country: Israel

institute: Tel Aviv University

summary: We applied in parallel RNA-Seq and Ribosome-profiling analyses to immortalized human primary BJ fibroblast cells under the following conditions: normal proliferation, quiescence (induced by serum depletion), senescence (induced by activation of the oncogenic RASG12V gene, and examined at early (5 days; pre-senescent state) and late (14 days; fully senescent state) time points), and neoplastic transformation (induced by RASG12V in the background of stable p53 and p16INK4A knockdowns and SV40 small-T expression.

overall_design:
RNA-seq, using Illumina HiSeq 2000, was applied to BJ cells under 5 conditions: proliferation, quiescence, pre-senescence, full-senescence, and transfomed.
Ribosome profiling, using Illumina HiSeq 2000, was applied to BJ cells under 5 conditions: proliferation, quiescence, pre-senescence, full-senescence, and transfomed.

first: Fabricio

last: Loayza-Puch

first: Rani

first: Reuven

last: Agami


title: Transcript structures in Shewanella loihica PV-4

summary: 5' RNASeq of mRNA from Shewanella loihica PV-4 grown aerobically in Luria-Bertani broth (LB) and defined lactate minimal medium


title: Transcript structures in Shewanella sp MR-7

summary: 5' RNASeq of mRNA from Shewanella sp MR-7 grown aerobically in Luria-Bertani broth (LB) and defined lactate minimal medium


title: Transcript structures in Shewanella amazonensis SB2B

summary: 5' RNASeq of mRNA from Shewanella amazonensis SB2B grown aerobically in Luria-Bertani broth (LB) and defined lactate minimal medium


title: Transcript structures in Shewanella sp MR-4

summary: 5' RNASeq of mRNA from Shewanella sp MR-4 grown aerobically in Luria-Bertani broth (LB) and defined lactate minimal medium


title: Cell-autonomous function of Runx1 transcriptionally regulates megakaryocytic maturation in mice

status: Public on Mar 22 2013

city: Rechovot

first: Ram

last: Jaschek

address: P.O Box 26

institute: Weizmann Institute of Science


title: Plants regenerated from tissue culture contain stable epigenome changes in rice

city: Dallas

first: Hume

last: Stroud

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern

summary:
Most transgenic crops are produced through tissue culture. The impact of utilizing such methods on the plant epigenome is poorly
understood. Here we generated whole-genome, single-nucleotide resolution maps of DNA methylation in several transgenic rice lines.
We found that all tested transgenic plants had significant losses of methylation compared to untransformed plants. Loss of methylation
was largely stable across generations, and certain sites in the genome were particularly susceptible to loss of methylation. Loss of
methylation at promoters was associated with deregulated expression of protein-coding genes. Analyses of callus and untransformed
plants regenerated from callus indicated that loss of methylation is stochastically induced at the tissue culture step. These changes in
methylation may explain a component of somaclonal variation, a phenomenon in which plants derived from tissue culture manifest
phenotypic variability.

overall_design:
Whole genome methylation maps of rice were generated using BS-seq (Hume Stroud, Suhua Feng, Steve Jacobsen at UCLA).
Whole genome expression maps of  rice were generated using mRNA-seq and smRNA (Stacey Simon, Blake Meyers at Univ of Delaware).

first: Stacey

last: Simon

first: Suhua

last: Feng

first: Blake

last: Meyers

first: Steven

middle: E

last: Jacobsen


title: Transcript structures in Shewanella oneidensis MR-1

summary: 5' RNASeq of mRNA from S. oneidensis MR-1 grown aerobically in Luria-Bertani broth (LB) and defined lactate minimal medium


title: Transcript structures in Shewanella putrefaciens CN-32

summary: 5' RNASeq of mRNA from Shewanella putrefaciens CN-32 grown aerobically in Luria-Bertani broth (LB) and defined lactate minimal medium


title: 5-hydroxymethylcytosine-mediated epigenetic modifications between iPSCs and hESCs

first: Tao

address: 615 Michael Street

institute: Emory University

summary: Mammalian somatic cells can be directly reprogrammed into induced pluripotent stem cells (iPSCs) by introducing defined sets of transcription factors. Somatic cell reprogramming involves epigenomic reconfiguration, conferring iPSCs with characteristics similar to embryonic stem (ES) cells. Human ES cells contain 5-hydroxymethylcytosine (5hmC), which is generated though the oxidation of 5-methylcytosine (5mC) by the TET family of enzymes. Here we show that 5hmC level increases significantly during reprogramming due to the activation of TET1. During this process, dynamic genome-wide 5hmC modification occurs across the genome with more modifications at telomere-proximal regions. Compared with hES cells, we found iPS cells tend to form large-scale (100kb-1.3Mb) aberrant reprogramming hotspots in subtelomeric regions, most of which display incomplete hydroxymethylation. Strikingly, these 5hmC aberrant hotspots largely coincide (>80%) with previously reported aberrant non-CG methylation regions. Our results suggest that 5hmC modification could play important roles during reprogramming to pluripotency, and contribute to the differences between iPSCs and hESCs.

overall_design: we generated comprehensive genome-wide profiles of 5hmC in somatic cells, iPS cell lines derived from a variety of origins, and multiple hES cell lines.


title: RNA-seq analysis of Xenorhabdus nematophila

first: Brian

last: Tjaden

summary: Analysis of size selected RNA samples to identify sRNAs using wild-type and rpoS mutant strains.

overall_design: Four experiments, two from each of two strains using two protocols.

first: H

last: Goodrich-Blair

first: X

last: Lu

first: B


title: Transcript structures in Shewanella sp ANA-3

first: Wenjun

summary: 5' RNASeq of mRNA from Shewanella sp ANA-3 grown aerobically in Luria-Bertani broth (LB) and defined lactate minimal medium

first: Morgan


title: Cell-autonomous function of Runx1 transcriptionally regulates megakaryocytic maturation in mice (ChIP-seq)

summary: RUNX1 transcription factor (TF) is a key regulator of megakaryocytic development and when mutated is associated with familial platelet disorder and predisposition to acute myeloid leukemia (FPD-AML). We used mice lacking Runx1 specifically in megakaryocytes (MKs) to characterize the Runx1-mediated transcriptional program during advanced stages of MK differentiation. Gene expression and chromatin-immunoprecipitation-sequencing (ChIP-seq) of Runx1 and p300 identified functional Runx1-bound MK enhancers. Runx1/p300 co-bound regions showed significant enrichment in genes important for MK and platelet homeostasis. Runx1-bound regions were highly enriched in RUNX and ETS motifs and to a lesser extent in GATA motif. The data provides the first example of genome-wide Runx1/p300 occupancy in maturating FL-MK, unravels the Runx1-regulated program controlling MK maturation in vivo and identifies its bona fide regulated genes. It advances our understanding of the molecular events that upon mutations in RUNX1 lead to the predisposition to familial platelet disorders and FPD-AML.

overall_design:
Examination of RUNX1 and P300 binding in WT mouse megakaryoctye cells using ChIP-Seq.

The supplementary 'GSE45372_PeakList.txt' file includes a list of regions identified as binding for P300 or RUNX1 or both.

first: Niv

last: Pencovich


title: RNAseq analysis of the serotype M1 group A Streptococcus strain MGAS2221

status: Public on Mar 20 2013

city: Reno

first: Paul

last: Sumby

state: NV

address: 1554 N. Virginia St.

department: Microbiology & Immunology

institute: University of Nevada

summary: We recovered RNA from exponential and stationary phase cell cultures of MGAS2221 and utilized two distinct methods to remove rRNA from our samples, the RiboZero kit from Epicenter, and the terminator- 5--Phosphate-Dependent Exonuclease (TEX).  This gave us 4 distinct RNAs with which we performed RNAseq analysis.  Both rRNA removal methods worked well, with only a small percentage of the final total read counts being derived from rRNA sequences.

overall_design: A single group A Streptococcus strain was investigated.


title: Global transcriptional role of CtBP in breast cancer cells

city: bethesda

first: Lijun

last: Di

address: 41 center dr

institute: NCI

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

first: Li-jun

first: Kevin

last: Gardner


title: Genome-wide maps of CtBP binding profile in breast cancer cell line MCF-7

summary: CtBP is a global co-repressor by serving as transcriptional factor in multiple pathways. CtBP functioned as transcriptional factor by recruiting other cofactors such as G9a, HDAC1 and PcG proteins. CtBP is found to be over enriched in several type of tumor samples. To dipict the role of CtBP in globally regulating gene expression, we applied ChIP-seq technology to find out the binding profile of CtBP in breast cancer cell line MCF-7. Our data suggest CtBP plays a global regulatory role in DNA damage repair, tumor initiation, and EMT process.

overall_design: Examine CtBP binding in MCF-7 cells


title: Comparison of stem-cell derived retinal pigment epithelia (RPE) with human fetal retina pigment epithelium

city: New Haven

first: Mei

last: Zhong

address: 10 Amistad Street

department: Stem Cell Center

institute: Yale University

summary: Retinal Pigment Epithelium (RPE) derived from two human embryonic stem cell lines, H1 and H9, were compared with human fetal RPE (hfRPE) using RNA-seq. Nominally, the transcriptome of H1-derived RPE showed greater overlap with hfRPE. For cells maintained in the medium used to differentiate RPE, 6.2% (H1-RPE) and 4.2% (H9-RPE) of the transcripts were expressed in amounts that were statistically different from hfRPE (false discovery rate: 5%).  After adaptation to the serum-free medium, SFM-1, only 1.0 % (H1-RPE) and 1.9% (H9-RPE) were expressed in amounts that were statistically different. For RPE signature genes, statistical differences were observed for 1.0 % (H1-RPE) and 1.9% (H9-RPE) of the transcripts. For some barrier-function related mRNAs the statistical differences were greater than these small differences would predict. For adhesion proteins and plasma membrane transporters, the differences were as great as 6.9% and 4.3%, respectively. After adaptation to SFM-1, the statistical differences between H1- and H9-RPE were only 0.4% for all transcripts, 1.4% for signature genes, and 0.7% for membrane transporters.  No statistical differences were observed for the transcripts related to tight junctions, adhesion junctions or ion channels. In summary, SFM-1 promoted the maturation of stem cell-derived RPE, and the statistical difference between two stem cell lines was minimal.

overall_design: RNA sequencing of hfRPE from three fetuses (reference sample) and three independent isolates of RPE derived from the H1, and three from the H9, human embryonic stem cell (hESC) lines. The cultures were maintained in a serum-free medium, SFM-1.  Comparisons were also made to cultures maintained in the medium used to differentiate the cells, KSR.

first: Lawrence

last: Rizzolo

first: Shaomin

last: Peng

first: Geliang

last: Gan

first: Hongyan

last: An


title: EBF2 determines and maintains brown adipocyte identity

status: Public on Mar 18 2013

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

summary: We compared PPARg binding sites in BAT and eWAT to identify regulatory elements that contribute to BAT identity and to find an important factor that bind those elements. To this end, we performed PPARg ChIP-seq in both tissues and called each tissue-spsecific binding sites.

overall_design: PPARg ChIP-seq in BAT and eWAT of mice

first: Sona

last: Rajakumari

first: Jeff

last: Ishibashi

first: Kyoung-Jae

last: Won

first: Parick

last: Seale


title: Gene expression and 5hmC/5mC state in pluripotent and TSKM-iPS induction cells

city: Beijing

first: Tao

last: Cai

address: No. 7 Science Park Road, Zhongguancun Life Science Park

institute: National Institute Of Biological Sciences, Beijing (NIBS)


title: Genome-wide maps of 5hmC/5mC state in pluripotent and (T-)iPS induction cells.

summary: We performed 5hmC/5mC DNA Immunoprecipitation followed high-throughput sequencing using the cell sample along the whole TSKM secondary reprogramming system. The TSKM 0D is the fibroblasts deried from TSKM-iPS mouse as the starting cells of the reprogramming.The intermediate cells is 3-days induced cells which are refered as TSKM 3D cells, and the final reprogrammed cells is the iPS cells with full pluripotency driven from this secondary system. We compared the profiling of 5-hydroxymethylcytosine and 5-methylcytosine modifications in these different cell lines. We found that:  a widespread accompanying increase of 5hmC and 5mC at TSS and ES-active regulation regions followed by 5mC-5hmC pattern switch. Taking the advantage of the newly established TSKM secondary reprogramming system, the epigenetic remodeling and regulation mechanisms can be further investigated to advance our understanding of the epigenetic barriers and decipher the dynamic mechanism in somatic cell reprogramming.

overall_design: Examination of 5-hydroxymethylcytosine/5-methylcytosine modifications in a Tet1-mediated secondary reprogramming system

first: Yawei

last: Gao

first: Jiayu

last: Chen

first: Shaorong


title: Conservation and Divergence of Transcriptomic and Epigenomic Variations in Maize Hybrids

status: Public on Mar 19 2013

first: Xuncheng

last: Wang

address: 5 Yiheyuan Road

institute: Peiking University

summary: The complexity of the maize (Zea mays) genome makes it an ideal system for the study of both genetics and epigenetics. Here, we generated the integrated maps of transcriptomes and epigenomes of shoots and roots of two maize inbred lines and their reciprocal hybrids, and globally surveyed the epigenetic variations and their relationships with transcriptional divergence between different tissues and different genotypes. We observed that whereas histone modifications vary both between tissues and between genotypes, DNA methylation patterns are more distinguishable between genotypes than between tissues. Histone modifications were associated with transcriptomic divergence between tissues and between hybrids and parents. Further, we show that genes up-regulated in both shoots and roots of hybrids were significantly enriched in the nucleosome assembly pathway. Interestingly, 22- and 24-nt siRNAs were shown to be derived from distinct transposable elements (TEs), and for different TEs in both shoots and roots, the differences in siRNA activity between hybrids and patents were primarily driven by different siRNA species. Together, our results suggest that despite of the variations in specific genes or genomic loci, similar mechanisms may account for the genome-wide epigenetic regulation of gene activity and transposon stability in different tissues of maize hybrids.

overall_design: Genome-wide integrated maps of mRNA and small RNA (sRNA) transcriptomes, DNA methylomes and genome-wide distribution of three representative histone modifications (H3K4me3, H3K9ac and H3K36me3) in the shoots and roots of 14 day old seedlings of two maize inbred lines (B73 and Mo17) and their reciprocal hybrids (B73 x Mo17 and Mo17 x B73).

first: Guangming

last: He

first: Xingwang

last: Deng


title: mRNA profiling of GGT-HIF2aM3 (gamma-HIF2alphaM3) kidney cortex

city: New York

first: Leiping

last: Fu

state: NY

address: 1300 York Avenue

department: Pharmacology

institute: Weill Cornell Medical College

summary: The complete transcriptomes of kidney cortex from 3 γ-HIF2αM3 18 month old TG+ male mice and 3 age matched wild type (WT) C57BL/6 male mice were sequenced on an Illumina HiSeq2000 Sequencer.

overall_design: Examination of complete transcriptome of kidney cortex between γ-HIF2αM3 TG+ male mice and wild type C57BL/6 male mice

first: David

last: Nanus

first: Lorraine

last: Gudas


title: Amplitude modulation of androgen signaling by c-MYC [ChIP-Seq]

status: Public on Mar 16 2013

city: Houston

first: Yiwen

address: 1400 Pressler Street

department: Bioinformatics and Computational Biology

institute: University of Texas MD Anderson Cancer Center

summary: Androgen-stimulated growth of the molecular apocrine breast cancer is mediated by an androgen receptor (AR)-regulated transcriptional program.  Through profiling the genomic licalizations of AR and its co-regulators FOXA1 and TCF7L2 in MDA-MB-453 breast cancer cells, we revealed the molecular details of the AR-centered regulatory network. We further identified that  c-MYC is a key downstream target co-regulated by AR, FOXA1 and TCF7L2, and reinforces the transctiopnal activation of androgen-responsive genes in this subtype of breast cancers.

overall_design: AR and FOXA1 ChIP-seq were performed in MDA-MB-453 breast cancer cells with treatment of 5a-dihydrotestosterone (DHT) for 16 h. TCF7L2 ChIP-seq was performed in MDA-MB-453 cells treated with vehicle or DHT for 16 h, respectively. MYC ChIP-seq was performed in MDA-MB-453 cells following 6 h DHT stimulation.

first: Min

last: Ni

first: Myles

last: Brown


title: Methylome of Salmonella enterica subsp. Enterica serovar Javiana str. CFSAN001992 by PacBio SMRT Sequencing

status: Public on Mar 15 2013

city: College Park

first: Justin

middle: St. Giles

last: Payne

state: Maryland

address: 5100 Paint Branch Parkway

department: DM

institute: FDA/CFSAN

summary: Single-molecule read technologies allow for detection of epigenomic base modifications during routine sequencing by analysis of kinetic data during the reaction, including the duration between base incorporations at the elongation site (the "inter-pulse duration.") Methylome data associated with a closed de novo bacterial genome of Salmonella enterica subsp. enterica serovar Javiana str. CFSAN001992 was produced and submitted to the Gene Expression Omnibus.

overall_design: Single-sample sequencing and base modification detection of cultured isolate of a foodborne pathogen.

first: Tim

last: Muruvanda

first: Marc

last: Allard


title: Stability, Delivery and Functions of Human Sperm RNAs at Fertilization

status: Public on Mar 11 2013

city: Detroit

first: Stephen

last: Krawetz

state: MI

address: 275 E. Hancock

department: Center for Molecular Medicine and Genetics

institute: Wayne State University School of Medicine

summary: We report on abundance and transcript profile characteristics of sperm RNAs.

overall_design: Examination of RNA population and distribution in spermatozoa

first: Edward

middle: D

last: Sendler

middle: A


title: Systematic dissection of regulatory motifs in 2,000 predicted human enhancers using a massively parallel reporter assay

city: Cambridge

first: Tarjei

middle: S

last: Mikkelsen

address: 7 Cambridge Center

institute: Broad Institute

summary: We employ a massively parallel reporter assay (MPRA) to measure the ex vivo activities of hundreds of K562 and HepG2 enhancers with known transcription factor motif instances. For seven selected motifs that correspond to known or predicted activators and repressors in the two cell types, we make directed modifications of the bases corresponding to these motifs and observe the changes in enhancer activity.

sample_organism:
Escherichia coli
Homo sapiens

platform_organism:
Escherichia coli
Homo sapiens

overall_design: Reporter mRNA-seq from HepG2 and K562 cells transfected with a ~55,000-plex MPRA plasmid pool containing 5,418 mutated human enhancer sequences, each linked to 10 distinct 10-nt tags. The reporter mRNA tags facilitate quantitation of their abundances. The same tags were also sequenced from the transfected MPRA plasmid pool to facilitate normalization to plasmid copy numbers.

first: Pouya

last: Kheradpour

first: Jason

last: Ernst

first: Manolis

last: Kellis


title: The Role of Tet1 During Somatic Cell Reprogramming

status: Public on Mar 08 2013

city: Guangzhou

first: Lihui

last: Lin

state: Guangdong

address: No.190, Kaiyuan Street

department: Stem cell

institute: Guangzhou Institutes Of Biomedicine and Health Chinese Academy Of Science

summary: Tet1 is a hydroxylase known for its role in the conversion of 5-methylcytosines (5mC) to 5-hydroxymethylcytosines (5hmC) involved in the possible active demethylation process and gene expression regulation. As somatic cell reprogramming involves the re-activation of pluripotency genes and the silencing of somatic ones, it remains unclear the role of Tet1 in the reprogramming process. Here, we performed hMeDIP-seq and RNA-seq during somatic cells reprogramming with Tet1 over expression to invest the effect of Tet1.

overall_design: Examination of genome DNA hmC modifications in 2 conditions: individually overexpressed Tet1CD or Tet2CD during MEF reprogramming; Examination of mRNA levels in five different conditions: individually overexpressed DR or Tet1CD or Tet1CDmut or Tet2CD or Tet2CDmut, during MEF reprogrammig.

first: Duanqing

last: Pei

first: Guo-Liang

last: Xu


title: Transcriptome of chronic myeloid leukemia blood in early disease based on RNA-seq method

city: Jiangyin

first: JianBo

last: Zhou

state: Jiangsu

address: Shou Road No. 163

institute: People's Hospital of Jiangyin City

summary: In order to support our research of chronic myeloid leukemia in human genome, we conducted massively parallel pyrosequencing of mRNAs (RNA-seq) using chronic myeloid leukemia blood in early disease. We obtained a total of 17.74 million read pairs from blood in early disease.The RNA-seq data derived from the sample illustrated the expreesion genes in chronic myeloid leukemia blood in early disease of human.

overall_design: 1 sample examined: blood in early disease.


title: Next-generation sequencing identifies mRNAs targets that experience significant changes in alternative splicing upon PQBP1 knockdown in mouse embryonic cortical neurons

city: Berkeley

first: Qingqing

last: Wang

address: 161 Koshland Hall, UC Berkeley

institute: University of California, Berkeley

summary: PQBP1 is a highly conserved protein closely related to neurodegenerative disorders. We identified PQBP1 as an important alternative splicing effector necessary for maintaining normal neuron functions in the brain. In order to explore PQBP1's functions in alternative splicing regulation and neuronal activities, we systematically profiled the alternative splicing targets of PQBP1 in mouse embryonic cortical neurons by RNA-seq. The mRNAs whose alternative splicing are affected by PQBP1 showed tissue-specific functional enrichment especially in neurite outgrowth, with strong Gene Ontology (GO) enrichments for neuron projection development/morphogenesis, dendrite development and axonogenesis. PQBP1's alternative splicing targets are also functionally enriched in RNA splicing, chromatin modification, and ARF signal transduction.

overall_design: We applied RNA-seq to compare the transcriptomes of mock and PQBP1 knockdown mouse embryonic cortical neuron samples.

first: Pamela

last: Silver


title: PRC1 coordinates timing of sexual differentiation of female primordial germ cells (RNA-Seq)

status: Public on Mar 14 2013

city: Basel

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

country: Switzerland

institute: FMI

summary: In mammals, sex differentiation of primordial germ cells (PGCs) is determined by extrinsic cues from the environment1. In female PGCs, expression of Stimulated by retinoic acid 8 (Stra8) and meiosis are induced in response to retinoic acid (RA) provided by the mesonephroi2-4. Given the widespread role of RA signaling during development8,9, the molecular mechanism specifying the competence of PGCs to timely express Stra8 and enter meiosis are unknown2,10. Here we identify gene dosage dependent roles in PGC development for Ring1 and Rnf2, two central components of the Polycomb Repressive Complex 1 (PRC1)11,13. Both paralogs are essential for PGC development between day 10.5 and 11.5 of gestation. Rnf2 is subsequently required in female PGCs for maintaining high levels of Oct4 and Nanog expression6, and for preventing premature induction of meiotic gene expression and entry into meiotic prophase. Chemical inhibition of RA signaling partially suppresses precocious Oct4 down-regulation and Stra8 activation in Rnf2-deficient female PGCs. Chromatin immunoprecipitation analyses show that Stra8 is a direct target of PRC1 and PRC2 in PGCs. These data demonstrate the importance of PRC1 gene dosage in PGC development and in coordinating the timing of sex differentiation of female PGCs by antagonizing extrinsic RA signaling.

overall_design: Gene expression of mouse primordial germ cells was analysed using RNAseq method. Primodial germ cells were purified from embryos carrying Oct4(-delta-PE)-GFP transgene by FACS.

first: Shihori

last: Yokobayashi

first: Hubertus

last: Kohler

first: Peter

last: Nestorov

first: Kirsten

last: Jacobeit

first: Antoine

middle: H

last: Peters


title: MeCP2-R270X and MeCP2-G273X ChIP-Seq

status: Public on Mar 12 2013

first: Peng

last: Yu

address: 1 Baylor Plaza

institute: BCM

summary: MECP2-R270X transgenic mice (TG) and MECP2-G273X TG mice were generated in the Zoghbi Lab. These mice express the respective truncated form of MeCP2 tagged with GFP at the C-terminus from a transgenic human PAC containing all known regulatory sequences. These transgenes were maintained on a wild-type pure FVB background. For experiments each transgenic line was crossed by Mecp2 null mice (Mecp2 tm1.1Bird)  on a pure 129SvEv background and the resulting male F1 hybrid progeny (FVB;129SvEv) that lacked endogenous MeCP2 expression but expressed either transgene (Mecp2 -/y; MECP2-R270X TG or Mecp2-/y; MECP2-G273X TG) were used for ChIP-Seq analysis. Whole brain from either the R270X mice (Mecp2 -/y; MECP2-R270X TG) or the G273X mice (Mecp2 -/y; MECP2-G273X TG) was formaldehyde crosslinked and purified chromatin was immunoprecipitated with anti-GFP antibody (Abcam ab6556).

overall_design: 2 samples: R270X (Mecp2 -/y; MECP2-R270X TG) and G273X (Mecp2 -/y; MECP2-G273X TG) both on an F1 (FVB;129SvEv) hybrid background

first: Steven

last: Baker

first: Huda

last: Zoghbi


title: Genome-wide profiling of miRNAs and their target genes during somatic embryogenesis in cotton by small RNA and degradome sequencing

city: Wuhan

first: Xiyan

last: Yang

state: Hubei

address: Shizishan 1, Hongshan

institute: Huazhong Agricultural University

summary: MicroRNAs (miRNAs) are endogenous non-coding ~21 nucleotide (nt) RNAs that regulate gene expression at transcriptional and post-transcriptional levels in plants and animals. They play an important role in development, abiotic stress responses or pathogen responses. miRNAs with their related target genes have been widely studied in model plants，and increasing studies have been performed on some crops，however, the number of identified miRNAs in cotton was limited, and global identification of related targets through degradome sequencing has not been developed previously. In this study, we globally identified small RNAs and their related target genes during cotton somatic embryogenesis by the high throughput small RNA and degradome sequencing technology using fresh hypocotyls and EC (embryogenic calli) of Gossypium hirsutum YZ1. A total of 36 differentially expressed conserved miRNA families of which 19 miRNA families represented by 29 precursors and 25 novel miRNAs were identified, with star sequences of 20 known miRNAs and 2 novel miRNAs discovered. 234 genes in EC and 322 genes in CK were identified as targets of 23 and 30 known miRNA families, and 16 genes were found as targets of 8 novel miRNAs.  The expression profiles of several miRNAs and their targets were verified by qRT-PCR and 5’RACE were further used to validate the sliced sites of the targets. Interestingly, four TAS3 D6 and D7 were also found in both degradome libaries which can perfectly match their precursors. The profiling of the miRNAs and their target genes provides more information about the regulatory network of miRNAs during somatic embryogenesis in cotton.

overall_design: small RNA and degradome sequencing of CK(fresh hypocotyls) and EC (embryogenic calli) of Gossypium hirsutum YZ1

first: Lichen

first: Xianlong

last: Zhang

first: Daojun

last: Yuan


title: Reconstruction of the dynamic regulatory network that controls Th17 cell differentiation by systematic perturbation in primary cells (ChIP-Seq)

status: Public on Mar 07 2013

first: Nir

last: Yosef

address: Berkeley

department: EECS

institute: UC Berkeley

summary: Despite their enormous importance, the molecular circuits that control the differentiation of Th17 cells remain largely unknown. Recent studies have reconstructed regulatory networks in mammalian cells, but have focused on short-term responses and relied on perturbation approaches that cannot be applied to primary T cells. Here, we develop a systematic strategy – combining transcriptional profiling at high temporal resolution, novel computational algorithms, and innovative nanowire-based tools for performing gene perturbations in primary T cells – to derive and experimentally validate a temporal model of the dynamic regulatory network that controls Th17 differentiation. The network is arranged into two self-reinforcing and mutually antagonistic modules that either suppress or promote Th17 differentiation. The two modules contain 12 novel regulators with no previous implication in Th17 differentiation, which may be essential to maintain the appropriate balance of Th17 and other CD4+ T cell subsets. Overall, our study identifies and validates 39 regulatory factors that are embedded within a comprehensive temporal network and identifies novel drug targets and organizational principles for the differentiation of Th17 cells.

overall_design: DNA binding of TSC22D3 in Th17 cells compared to WCE

first: Aviv

last: Regev


title: HITS-CLIP analysis of FMRP mRNA binding sites from P11-P25 mouse brain polysomes

first: Jennifer

last: Darnell

address: 1230 York Ave.

institute: The Rockefeller University

summary: FMRP loss-of-function causes Fragile X Syndrome (FXS) and autistic features.  FMRP is a polyribosome-associated neuronal RNA-binding protein, suggesting that it plays a key role in regulating neuronal translation, but there has been little consensus regarding either its RNA targets or mechanism of action.  Here we use high throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP) to identify FMRP interactions with mouse brain polyribosomal mRNAs. FMRP interacts with the coding region of transcripts encoding pre- and postsynaptic proteins, and transcripts implicated in autism spectrum disorders

overall_design: Polyribosomes were prepared from UV254-crosslinked pooled littermate FVB mouse brains as described in detail in published paper PMID 21784246.  Polyribosomes were dissociated under denaturing conditions using two different protocols to disrupt ribonucleoprotein complexes. In most experiments Fmr1-null littermates were used in parallel to confirm FMRP specificity.  After mild RNAse treatment to reduce the size of RNA to 60-100 nucleotides, endogenous FMRP was immunoprecipitated with one of two antibody combinations, either mixed monoclonal antibodies 7G1-1 and 2F5, or polyclonal antibody ab17722 (Abcam).  The ages of the mice were P11, P13, P14, P15, and P25.  In addition, to assess a different neuronal polysome-associated protein, as another control, lysates prepared from two samples, the P11 and P13 mice, were split in half and one half IPed with a human anti-Hu antisera as the neuronal Hu proteins are polysome-associated in brain.  In sum, 7 FMRP HITS-CLIP experiments were performed including (1) P14 mouse polysomes prepared by Protocol 1 and IPed with 7G1-1/2F5 (2) P14 mouse polysomes prepared by Protocol 1 and IPed with ab17722 (3) P15 mouse polysomes prepared by Protocol 1 and IPed with 7G1-1/2F5 (4) P25 mouse polysomes prepared by Protocol 1 and IPed with 7G1-1/2F5 (5) P25 mouse polysomes prepared by Protocol 1 and IPed with ab17722 (6) P11 mouse polysomes prepared by Protocol 2 and IPed with ab17722 and (7) P13 mouse polysomes prepared by Protocol 2 and IPed with ab17722. FMRP-bound or Hu-bound RNA tags were cloned and submitted for high throughput sequencing on the Life Science 454 platform (samples 1-5) or the Illumina platform (samples 6 and 7 and the 2 Hu samples processed in parallel with samples 6 and 7). Full details are given in PMID 21784246.

first: Chaolin

first: Robert


title: Reconstruction of the dynamic regulatory network that controls Th17 cell differentiation by systematic perturbation in primary cells (RNA-Seq)

overall_design: RNA-seq of knockdown of 12 genes in Th17 cell differentiation


title: Reconstruction of the dynamic regulatory network that controls Th17 cell differentiation by systematic perturbation in primary cells

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

overall_design: Refer to individual Series


title: Using RNA-Seq to Profile Soybean Seed Development from Fertilization to Maturity

city: Urbana

first: Lila

middle: O.

last: Vodkin

state: IL

address: 1201 W. Gregory Dr.

department: Crop Sciences

institute: University of Illinois

summary: To understand gene expression networks leading to functional properties and compositional traits of the soybean seed, we have undertaken a detailed examination of soybean seed development from a few days post-fertilization to the mature seed using Illumina high-throughput transcriptome sequencing (RNA-Seq). RNA was sequenced from seven different stages of seed development, yielding between 12 million and 78 million sequenced transcripts. These have been aligned to the 79,000 gene models predicted from the soybean genome recently sequenced by the Department of Energy Joint Genome Institute. Over one hundred gene models were identified with high expression exclusively in young seed stages, starting at just four days after fertilization. These were annotated as being related to many basic components and processes such as histones and proline-rich proteins. Genes involved with some storage proteins such as glycinin and beta-conglycinin had their highest expression levels at the stages of largest fresh weight, confirming previous knowledge that these storage products are being rapidly accumulated before the seed begins the desiccation process. Other gene models showed high expression in the dry, mature seeds, perhaps indicating the preparation of pathways needed later, in the early stages of imbibition. Many highly-expressed gene models at the dry seed stage are, as expected, annotated as hydrophilic proteins associated with low water conditions, such as late embryogenesis abundant (LEA) proteins and dehydrins, which help preserve the cellular structures and nutrients within the seed during desiccation. Hundreds of transcription factors with notable expression in at least one stage of seed development were also identified and examined. Results from a second biological replicate demonstrate high reproducibility of these data.

overall_design: High-throughput sequencing using Illumina Genome Analyzer II and Illumina HiSeq 2000 (RNA-Seq) was performed on seven stages of soybean seeds, with two biological replicates per stage.

first: Sarah

middle: I

last: Jones

middle: O


title: Phytoplasma-responsive small RNAs in Mexican lime trees

status: Public on Mar 09 2013

city: Roanoke

first: Aboozar

last: Monavarfeshani

state: VA

address: 2 Riverside Circle

department: Biological Science

institute: Virginia Tech

summary:
Background: Witches’ broom disease of Mexican lime (Citrus aurantifolia L.), which is caused by the phytoplasma “Candidatus Phytoplasma aurantifolia”, is a devastating disease that results in significant economic losses. Plants adapt to abiotic stresses by regulating gene expression at the transcriptional and post-transcriptional levels. MicroRNAs (miRNAs) are a recently identified family of molecules that regulate plant responses to environmental stresses through post-transcriptional gene silencing.
Methods: Using a high-throughput approach to sequence small RNAs, we compared the expression profiles of miRNAs in healthy Mexican lime trees and in plants infected with “Ca. Phytoplasma aurantifolia”.
Results: Our results demonstrated the involvement of different miRNAs in the response of Mexican lime trees to infection by “Ca. Phytoplasma aurantifolia”. We identified  miRNA families that are expressed differentially upon infection with phytoplasmas. Most of the miRNAs had variants with small sequence variations (isomiRs), which are expressed differentially in response to pathogen infection.
Conclusions: It is likely that the miRNAs that are expressed differentially in healthy and phytoplasma-infected Mexican lime trees are involved in coordinating the regulation of hormonal, nutritional, and stress signalling pathways, and the complex interactions between them. Future research to elucidate the roles of these miRNAs should improve our understanding of the level of diversity of specific plant responses to phytoplasmas.

overall_design: Small mRNA profiles of healthy (H) and Phytoplasma-infected Mexican lime trees were generated by deep sequencing, six replicate, using Illumina Hiseq2000

first: Farveh

last: Ehya

first: Laleh

last: Karimi Farsad

first: Mojtaba

last: Khayam Nekouei

first: Mohsen

last: Mardi

first: Ghasem

last: Salekdeh


title: Deep Sequencing of the Porcine Endometrial Transcriptome on Day 14 of Pregnancy

city: Lindau

first: Stefan

middle: Michael

last: Bauersachs

state: Zurich

address: Eschikon 27 EHB 23.1

department: Department for Farm Animals

institute: University of Zurich

summary: In pigs, conceptus attachment to the uterine surface epithelium starts around day 14 of pregnancy preceded by a pronounced vascularization at the implantation zones, initiating the epitheliochorial placentation. To characterize the complex transcriptome changes in the endometrium in the course of initial conceptus attachment deep sequencing of endometrial RNA samples of pregnant animals (n=4) and corresponding cyclic controls (n=4) was performed using Illumina RNA-Seq. The obtained sequence reads were mapped to the porcine genome and relative expression values were calculated for the analysis of differential gene expression. Statistical analysis revealed 1,933 differentially expressed genes (FDR 1%), 1,229 with higher and 704 with lower mRNA concentration in the samples from pregnant animals. Expression of selected genes was validated by the use of quantitative real-time RT-PCR. The RNA-Seq data were compared to results of a microarray study of bovine endometrium on day 18 of pregnancy and additional related data sets. Bioinformatics analysis revealed for the genes with higher mRNA concentration in pregnant samples strong overrepresentation particularly for immune-related functional terms but also for apoptosis and cell adhesion. Overrepresented terms for the genes with lower mRNA concentration in pregnant samples were related to extracellular region, ion transport, cell adhesion and lipid and steroid metabolic process. In conclusion, RNA-Seq analysis revealed comprehensive transcriptome differences in porcine endometrium between day 14 of pregnancy and corresponding cyclic endometrium and highlighted new processes and pathways probably involved in regulation of non-invasive implantation in the pig.

overall_design: In total, 8 samples were analyzed, 4 biological replicates for pregnant animals (samples from 4 different animals) and 4 biological replicates for cyclic controls (samples from 4 different animals)

first: Anastazia

last: Samborski

first: Alexander

last: Graf

last: Krebs

first: Barbara

last: Kessler


title: Amplitude modulation of androgen signaling by c-MYC [RNA-Seq]

first: Yiwen

last: Chen

overall_design: MDA-MB-453 breast cancer cells were transfected with control of MYC siRNA for 48 h, followed by treatment with 10nM DHT or vehicle for 6 h. The cells were subjected to mRNA purification and library praparation for RNA-seq on Illumina HiSeq2000 platform.

first: Min

last: Ni

first: Teng

last: Fei

first: Myles

last: Brown


title: Amplitude modulation of androgen signaling by c-MYC


title: Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers

first: Richard

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research


title: Global transcriptional and phenotypic analyseis of Escherichia coli O157:H7 strain Xuzhou21 and its pO157_Sal cured mutant

status: Public on Mar 05 2013

first: qing

middle: hong

last: zhao

address: changbai road 155

institute: china cdc

summary: Escherichia coli O157:H7 is an important food-borne pathogen that can cause hemorrhagic colitis (HC) and hemolytic-uremic syndrome (HUS) in humans. pO157_Sal, a novel conjugative plasmid is present in a Chinese O157:H7 outbreak strain Xuzhou21. Here we investigated the phenotypic and transcriptional differences between the wild type strain Xuzhou21 and the pO157_Sal cured mutant strain Xuzhou21m. RNA-seq analysis found that all 52 ORFs encoded on pO157_Sal were transcribed. 168 chromosomal and pO157 genes were differentially expressed (≥2 fold difference) between Xuzhou21 and Xuzhou21m. Sixty-seven and 101 genes were up-regulated and down-regulated respectively by pO157_Sal including genes related to stress response, adaption and virulence. The plasmid-cured mutant grew slower than wild type in M9 medium under the condition of high NaCl or presence of sodium deoxycholate (NaDC), corroborating with the RNA-seq data. Seven differentially expressed genes are associated with NaDC resistance, including the adenine-specific DNA-methyltransferase gene (dam), multidrug efflux system subunit gene mdtA, hyperosmotically inducible periplasmic protein gene osmY and oxidation-reduction related genes while two differentially expressed genes (osmY and pspD) are likely to be related to resistance to osmotic pressure. A number of differentially expressed genes were virulence associated including four genes encoding T3SS effectors from the chromosome and ehxD from pO157. These findings demonstrated that the plasmid pO157_Sal affects the chromosome and pO157 genes transcription and contributes to the enhanced ability to resist stress. We conclude that pO157_Sal plays an important role in regulating global gene expression and affects virulence and adaptation of E.coli O157:H7.

overall_design: The total mRNA extracted from Escherichia coli O157:H7 Xuzhou21 and its plasmid cured strain Xuzhou21m were sequenced using Illumina.

first: Hongqing

last: ZHAO

first: Jianguo

last: XU


title: Genome-wide occupancy profile of Tbx3 in adult mouse whole heart

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

country: Netherlands

institute: Amsterdam UMC

summary: The contraction pattern of the heart relies on the activation and conduction of the electrical impulse. Perturbations of cardiac conduction have been associated with congenital and acquired arrhythmias as well as cardiac arrest. The pattern of conduction depends on the regulation of heterogeneous gene expression by key transcription factors and transcriptional enhancers. Here, we assessed the genome-wide occupation of conduction system–regulating transcription factors TBX3 in the mouse heart, uncovering cardiac enhancers throughout the genome.

overall_design: Examination of the cardiac transcription factor Tbx3 in adult mouse heart

first: Malou

last: van den Boogaard

first: Phil

last: Barnett


title: Bombyx mori Argonaute2 associated small RNAs

city: Hangzhou

first: Nie

last: Zuoming

state: Zhejiang

address: Xiasha high Education Zone, No.2 Road

department: School of Life Science

institute: Zhejiang Sci-Tech University

summary: As important roles of small RNA pathways, AGO proteins mediate interaction of incorporated small RNAs with their targets. The resolution of AGO associated small RNAs showed a significant landscape of AGO proteins and their binding small RNAs. To characterize small RNAs that associated with BmAGO2 protein in Bombyx mori, the small RNA population associated with BmAGO2 in BmN cells was extracted from the AGO immunoprecipitated complex and the small RNAs between 17nt to 50nt separated by a polyacrylamide gel electrophoresis were subjected to library construction and deep sequencing.The high throughput sequencing yielded a total of 11691441 reads, representing 813,702 unique reads with a abundance from 5731905 to 1.

overall_design: Small RNA associated with AGO2 of BmN cell infected with ie1-bacmid recombinant viruses were performed by high-throughput using Hiseq 2000.

first: Zuoming

last: Nie


title: Translatome of A549, H1299 and HBE cells

first: Gong

last: Zhang

address: Huang-Pu Avenue West 601

department: Institute of Life and Health Engineering

institute: Jinan University

summary: We performed translatome and transcriptome sequencing of A549, H1299 and HBE cells and analyzed the translation ratio (TR) of all genes

overall_design: Total RNA and ribosome-bound RNA were extracted from A549, H1299 and HBE cells, and the polyA+ mRNA was sequenced using Illumina GAIIx and HiSeq-2000. The reads were mapped to RefSeq RNA reference sequences and the expression level were quantified by rpkM calculation.

first: Tong

last: Wang

first: Yizhi

last: Cui

first: Jingjie

last: Jin

first: Jiahui

last: Guo

first: Guibin

first: Xingfeng

last: Yin

first: Qing-Yu

last: He


title: MicroRNA sequence and expression analysis of rat liver tissue exposed to aflatoxin B1 by deep sequencing

city: Fuzhou

first: Weiqiang

last: Yang

address: Shang Xia Dian 15

department: The Ministry of Education Key Laboratory of Biopesticide and Chemical Biology

institute: Fujian agriculture and forestry  university

summary: We report the application of illumina deep sequencing technology for high-throughput profiling of microRNA in aflatoxin B1 treated rat liver tissue, as well as normal liver tissue. miRNAs of miR-17-92 cluster, thought to be tumor activating miRNAs, were down-regulated. miR-34a, considered to be a tumor suppressor, was up-regulated.Novel miRNAs and miRNA base alteration caused by SNP or editing were predicted and summarized.

overall_design: Examination of 2 microRNA profiles in 2 liver tissues under different treatments.

first: Shihua

first: Junwei

last: Lian


title: Genome-wide comparison of DNA hydroxymethylation in mouse embryonic stem cells and neural progenitor cells by relative quantitative hMeDIP-seq

city: Shanghai

first: Yang

last: Shi

address: NO. 138, Yi-Xue-Yuan Road

institute: Fudan university

summary: DNA hydroxymethylation (5hmC) represents a new layer of epigenetic regulation in addition to DNA methylation (5mC). The genome-wide patterns of 5hmC distribution in many tissues and cells have recently been revealed by hydroxymethylated DNA immunoprecipitation (hMeDIP) followed by high throughput sequencing or tiling arrays. However, the DNA hydroxymethylome data generated by the conventional hMeDIP-seq method can not be used for direct quantitative comparison across different samples. In this study, we report a new quantitative hMeDIP-seq method, which uses barcode technology to label different DNA samples and performs hMeDIP-seq for multiple samples in one reaction system. Using this new method, we profiled and compared the DNA hydroxymethylomes of mouse ES cells (ESCs) and mouse ESCs-derived neural progenitor cells (NPCs). 5hmC levels around TSS in either ESCs or NPCs had negative correlation with gene expression levels，while 5hmC levels at gene body regions had different correlation with gene expression, depending on cell types. We identified differential hydroxymethylated regions (DHMRs) by comparing the 5hmC density of all 5hmC peaks between ESCs and NPCs. Many selected DHMRs (e.g., Ankrd23, Hist1h2aa, Fbxw7, and Epha2) were validated by hMeDIP-qPCR. Furthermore, we analyzed the relationship between the alteration of DNA hydroxymethylation and the gene expression change during neural differentiation, and our data suggest that both up- and down-regulated genes exhibited dramatic decrease in 5hmC during neural differentiation while the alteration of 5hmC had weak positive correlation with the changes in gene expression. Taken together, our data demonstrate that quantitative hMeDIP-seq is a powerful approach for genome-wide comparison of DNA hydroxymethylation across multiple samples. Importantly, the DHMRs between ESCs and NPCs uncovered in this study may provide clues for further investigation of the function of 5hmC in gene regulation and neural differentiation.

overall_design: Comparision of the genome-wide distribution of 5hmC in mouse embryonic stem cells and mouse ES-derived neural progenitor cells.

first: Li

last: Tan

first: Yujiang


title: Patterns of Population Epigenomic Diversity in Arabidopsis thaliana (RNA-Seq)

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

summary: Natural epigenetic variation provides a source for the generation of phenotypic diversity, but to understand its contribution to phenotypic diversity, its interaction with genetic variation requires further investigation. Here, we report population-wide DNA sequencing of genomes, transcriptomes, and methylomes of wild Arabidopsis thaliana accessions. Single cytosine methylation polymorphisms are unlinked to genotype. However, the rate of linkage disequilibrium decay amongst differentially methylated regions targeted by RNA-directed DNA methylation is similar to the rate for single nucleotide polymorphisms. Association analyses of these RNA-directed DNA methylation regions with genetic variants identified 2,372 methylQTL, which revealed the first population estimate of genetically dependent methylation variation. Analysis of invariably methylated transposons and genes across this population indicates that loci targeted by RNA-directed DNA methylation are epigenetically reactivated during male gametogenesis, which facilitates their silencing across generations.

overall_design: RNA-seq from naturally-occurring Arabidopsis accessions

first: Robert

middle: J

last: Schmitz

first: Matthew

last: Schultz


title: Histone variant, H2B.Z demarcates the AT-rich promoter regions of the Plasmodium falciparum genome

city: Nijmegen

last: Stunnenberg

address: Geert Grooteplein 28

department: Department of Molecular Biology (274)

institute: Radboud University

summary: Histone variants are key components of the epigenetic code and evolved to perform specific functions in transcriptional regulation, DNA repair, chromosome segregation and other fundamental processes. H2B.Z is a rare, apicomplexan-specific variant of histone H2B. Here we show that in Plasmodium falciparum H2B.Z localises to euchromatic intergenic regions throughout intraerythrocytic development and together with H2A.Z forms a double-variant nucleosomes subtype. These nucleosomes are enriched in promoters over 3’ intergenic regions and their occupancy generally correlates with the strength of the promoter, but not with its temporal activity. Remarkably, H2B.Z occupancy levels exhibit a clear correlation with the base-composition of the underlying DNA, raising the intriguing possibility that the extreme AT-content of the intergenic regions within the Plasmodium genome might be instructive for histone variant deposition. In summary, our data shows that the H2A.Z/H2B.Z double-variant nucleosome demarcates putative regulatory regions of the P. falciparum epigenome and likely provides a scaffold for dynamic regulation of gene expression in this deadly human pathogen.

overall_design: Genome-wide localization of H2B.Z has been studied at three stages of intraerythrocytic development by Illumina sequencing of chromatin-immunoprecipitated and input DNA.

first: Wieteke

last: Hoeijmakers

first: Adriana

last: Salcedo-Amaya

first: Arne

last: Smits

first: Kees-Jan

last: Françoijs

first: Moritz

last: Treeck

first: Tim-Wolf

last: Gilberger

first: Hendrik

middle: G

first: Richárd

last: Bartfai