title: Analysis of the melon (Cucumis melo) small RNAome by high-throughput pyrosequencing

city: Espinardo

first: Daniel

last: Gonzalez-Ibeas

state: Murcia

address: Campus de Espinardo s/n

department: Biologia Estres y Patologia Vegetal

country: Spain

institute: CEBAS-CSIC

summary: Melon (Cucumis melo L.) is a commercially important fruit crop that is cultivated worldwide. The melon research community has recently benefited from the determination of a complete draft genome sequence and the development of associated genomic tools, which have allowed us to focus on small RNAs (sRNAs). These are short, non-coding RNAs 21â24 nucleotides in length with diverse physiological roles. In plants, they regulate gene expression and heterochromatin assembly, and control protection against virus infection. Much remains to be learned about the role of sRNAs in melon. We constructed 10 sRNA libraries from two stages of developing ovaries, fruits and photosynthetic cotyledons infected with viruses, and carried out high-throughput pyrosequencing. We catalogued and analyzed the melon sRNAs, resulting in the identification of 26 known miRNA families (many conserved with other species), the prediction of 84 melon-specific miRNA candidates, the identification of trans-acting siRNAs, and the identification of chloroplast, mitochondrion and transposon-derived sRNAs. In silico analysis revealed more than 400 potential targets for the conserved and novel miRNAs. This analysis provides insight into the composition and function of the melon small RNAome, and paves the way towards an understanding of sRNA-mediated processes that regulate melon fruit development and melonâvirus interactions.

overall_design: 11 small RNA libraries from several tissues of melon are included en the raw data. 2 samples from ovary, 2 samples from fruit, 1 sample from healthy cotyledons (Cultivar Tendral), 1 samples from healthy cotyledons (genotype TGR-1551), 1 sample from cotyledons (cultivar Tendral) infected with Watermelon mosaic virus (WMV), 1 sample from cotyledons (cultivar TGR-1551) infected with WMV, 1 sample from cotyledons (cultivar Tendral) infected with Melon necrotic spot virus (MNSV, Malfa5 isolate), 1 sample from cotyledons (cultivar Tendral) infected with MNSV (chimeric virus with Malfa5-264 isolates), 1 library from synthetic RNA oligos. Raw reads were obtained from two independent 454 runs, ~22,000 reads each one, to a total of 447,180 reads

last: Blanca

first: Livia

last: Donaire

first: Montserrat

last: Saladie

first: Albert

last: Mascarell-Creus

first: Ana

last: Cano-Delgado

first: Jordi

last: Garcia-Mas

first: Cesar

last: Llave

first: Miguel

last: Aranda


title: Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression (RNA-Seq data)

status: Public on Aug 02 2011

city: Ann Arbor

first: Matthew

last: Iyer

state: MI

address: 5316 CCGC 0940 1400 E. Medical Center Drive

department: Michigan Center for Translational Pathology

country: USA

institute: University of Michigan

type: Expression profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

summary: Noncoding RNAs (ncRNAs) are emerging as key molecules in human cancer, with the potential to serve as novel markers of disease and to reveal uncharacterized aspects of tumor biology. Here we discover 121 unannotated prostate cancer–associated ncRNA transcripts (PCATs) by ab initio assembly of high-throughput sequencing of polyA+ RNA (RNA-Seq) from a cohort of 102 prostate tissues and cells lines. We characterized one ncRNA, PCAT-1, as a prostate-specific regulator of cell proliferation and show that it is a target of the polycomb repressive complex 2 (PRC2). We further found that patterns of PCAT-1 and PRC2 expression stratified patient tissues into molecular subtypes distinguished by expression signatures of PCAT-1–repressed target genes. Taken together, our findings suggest that PCAT-1 is a transcriptional repressor implicated in a subset of prostate cancer patients. These findings establish the utility of RNA-Seq to identify disease-associated ncRNAs that may improve the stratification of cancer subtypes.

overall_design: 21 prostate cell lines sequenced on the Illumina Genome Analyzer and GAII.  Variable number of replicates per sample.  RNA-Seq data from prostate cancer tissues used in this study will be made available on dbGAP.

first: Arul

middle: M

last: Chinnaiyan

first: John

last: Prensner


title: Replication initiation sites in cancer cells

city: Bethesda

first: Mirit

middle: I

last: Aladjem

state: MD

address: 37 Convent Dr. Building 37, Room 5068D

department: DNA Replication Group

institute: National Cancer Institute

summary: Reads from massively parallel sequencing of RNA primed, short nascent strands from asynchronously growing cancer cells (K562, MCF7, HCT116).

overall_design: Newly replicated DNA was isolated based on size (400-800 bp) and the presence of a short RNA stretch at the 5' end using lambda exonuclease. Purified nascent strands were analyzed using massively parallel sequencing. Sheared genomic DNA was sequenced as a control.

first: Haiqing

last: Fu

first: Melvenia

last: Martin

first: Michael

last: Ryan

first: RyangGuk

last: Kim

first: Owen

middle: K

last: Smith


title: Transcriptomic response to substrate and temperature in two thermophilic fungi, Myceliophthora thermophila and Thielavia terrestris, and a related mesophile, Chaetomium globosum

status: Public on Aug 08 2011

city: Montreal

first: Ian

last: Reid

state: QC

address: 7141 Sherbrooke West

department: Biology

country: Canada

institute: Concordia University

summary: The thermophilic filamentous fungi Myceliophthora thermophila (Sporotrichum thermophile) and Thielavia terrestris are proficient decomposers of cellulose, suggesting that they will be a rich source of thermostable industrial enzymes for lignocellulose degradation.  To identify the genes and proteins involved in this process, we explored the transcriptomes of M. thermophila and T. terrestris growing at 45 ºC on either glucose, alfalfa, or barley straw by short-read sequencing of extracted mRNA.  To better understand the adaptations that allow these fungi to grow at elevated temperatures, we compared their transcriptomes when growing at 34C to their transcritomes at 45C, and also to the transcriptome of the related fungus Chaetomium globosum, which does not grow at 45C.

sample_organism:
Chaetomium globosum
Thermothelomyces thermophilus
Thermothielavioides terrestris

overall_design: RNA was extracted from cultures in early growth stage growing with glucose, alfalfa, or barley straw as carbon source at 34C or 45C (M. thermophila and T. terrestris); duplicate cultures were sampled in some conditions.

first: Adrian

last: Tsang

first: Nadeeza

last: Ishmael

first: Nicholas

last: O'Toole


title: Genome-wide nucleosome position data for 3 yeast species

status: Public on Aug 01 2011

city: Boston

first: Alex

last: Tsankov

state: MA

address: 155 Bay State

institute: MIT

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Genome-wide nucleosome position data for wildtype and mutant strains in S. cerevisiae, C. albicans, and S. pombe

sample_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae
Candida albicans

overall_design: Illumina sequencing of mononucleosomal DNA isolated from mid-log cultures grown in rich medium (abbreviated CM, in house recipe). S. pombe samples were grown in YES medium at permissive temperature (30C) and restrictive temperature (35C)

first: Alexander

first: Nick

last: Rhind

first: Oliver

last: Rando

first: Aviv

last: Regev


title: High-throughput semi-quantitative analysis of insertional mutations in heterogeneous tumors

status: Public on Aug 12 2011

city: Amsterdam

first: Jos

last: Jonkers

email: j.jonkers@nki.nl, m.koudijs@nki.nl

address: Plesmanlaan 121

department: Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

type: Genome variation profiling by high throughput sequencing

summary: Exploiting the full potential of insertional mutagenesis screens with retroviruses and transposons requires methods for distinguishing clonal from subclonal insertion events within heterogeneous tumor cell populations. Current protocols, based on ligation mediated PCR, depend on endonuclease based fragmentation of genomic DNA, resulting in strong biases in amplification and sequencing due to a fixed product sizes of the amplicon. We have developed a method called shear-splink, which enables the semi-quantitative high-throughput sequence analysis of insertional mutations, enabling us to count the number of cells harboring a given integration, within a heterogeneous sample. The shear-splink method enriches for (sub)clonal integrations, thereby reducing the contribution of irrelevant passenger mutations normally hampering a reliable identification of common integration sites. Additionally, this improvement allows us to identify genetic interactions between affected genes, co-occurring mutations and to study acquired resistance mechanisms both in vivo and in vitro.

overall_design:
Sequencing of retrovrial integration sites by LM-PCR. The associated manuscript describes a new method to quantitatively determine retrovrial integration sites using an improved ligation-mediated PCR approach and subsequent 454 pyrosequencing.

[GSM562151 to GSM562159]: Sequence data from different mixtures of 2 different cell lines (called AE6 and BB12) which are processed without a restriction enzyme. These cell lines are derived from an MMTV induced mammary tumor, for which we amplify the MMTV integration sites using a ligation-mediated PCR setup. We mixed these 2 cell lines, both with a different integration spectrum, to determine whether our amplification and sequencing protocol is quantitative, meaning that the coverage per integration site is decreasing upon a further dilution of the sample.

[GSM641935 to GSM641950]: Unique Sleeping beauty induced lymphoma specimens (spleen) obtained from a cohort of 16 wild-type mice with the 129P2/C57BL/6J mixed background.

[GSM776576 to GSM776956]: The 379 submitted specimens are originating from 127 unique leukemia/lymphoma samples, processed using 3 different techniques in order to identify Sleeping Beauty integration sites.
We compared restriction enzyme based LM-PCR (RE-splink) with shearing based LM-PCR (shear-splink) on 127 unique Sleeping Beauty (SB) induced leukemia's/lymphomas. All  sequence data generated by the 454 sequencing platform are submitted to GEO, including the final output of our sequence analysis pipeline (in bed format; see Supplementary files linked below).
Previous submissions contained similar sequence information (integration sites of viruses or transposons driving tumorigenesis) and are all part of the same manuscript.

first: Marco

middle: J

last: Koudijs

first: Christiaan

last: Klijn

first: Louise

last: van der Weyden

first: Jaap

last: Kool

first: Jelle

last: ten Hoeve

first: Daoud

last: Sie

first: Pramudita

middle: R

last: Prasetyant

first: Eva

last: Schut

first: Sjors

last: Kas

first: Theodore

last: Whipp

first: Edwin

last: Cuppen

first: Lodewyk

last: Wessels

first: David

last: Adams


title: Global-gene expression of Phytophthora  phaseoli

city: Newark

first: Sridhara

middle: G

last: Kunjeti

state: DE

address: 531, S. college Ave

department: Plant and Soil Sciences

institute: University of Delaware

summary: Lima bean is an important vegetable processing crop to the Mid-Atlantic U.S. and is highly susceptible to the oomycete pathogen Phytophthora phaseoli, which causes downy mildew.  P. phaseoli resides in the same clade with the late blight pathogen, Phytophthora infestans.  Genetic resistance and fungicides are used to manage P. phaseoli and often fail.  Currently there are no molecular data on this pathosystem.  To rectify this situation and determine virulence mechanisms in P. phaseoli we performed a whole-transcriptome analysis using Illumina mRNA-Seq.  Six libraries were generated and compared, plate-grown and plant-grown.  Our data were normalized and were matched to the P. infestans gene models to obtain the abundance of the sequence reads.  This resulted in 10,427 P. phaseoli genes with homology to P. infestans and with expression in either one of the libraries.  Upon closer examination, 318 P. phaseoli-homologs matched either known or putative virulence genes in P. infestans.  We present data from the whole transcriptome as well as specifically chosen genes from this set of 318.  Interestingly, in six libraries from P. phaseoli we found a commonly expressed gene set of 66 out of 563 predicted RXLR genes in P. infestans.  The majority of the differentially expressed RxLR and elicitin-like were up-regulated in planta, while the reverse was true for crinkler homologs.  These results are discussed with respect to possible pathogenicity mechanisms in P. phaseoli and how they compare to P. infestans.

overall_design: Examination of 3 different conditions of Phytophthora phaseoli

first: Nicole

last: Donofrio

first: Thomas

middle: A

last: Evans

first: Nancy

middle: F

last: Gregory

first: Saritha

first: Blake

middle: C

last: Meyers

first: Venugopal

middle: S

last: Kalavacharla

first: Adam

last: Marsh


title: Response to temperature increase is genotype-dependent: A genomic analysis of marine larvae

city: Los Angeles

first: Jason

last: Curole

state: CA

address: 3616 Trousdale Pkwy.

department: Biological Sciences

institute: University of Southern California

summary: We produced differentially sensitive-temperature phenotypes using genetically defined larval families of the bivalve Crassostrea gigas.  Larval growth rates varied ~5-fold and reciprocal hybrids showed different genotype-dependent responses over a 15-25°C temperature range.  Whole-genome expression analysis of ~24 million cDNAs from larvae identified 22,250 unique transcripts.  Of these, ~15% showed a significant interaction between genotype and temperature and are associated with genotype-dependent differences in response to temperature.

overall_design: Examination of 2 genotypes of Pacific oyster larvae, grown at 3 temperatures

middle: P

first: Donal

middle: T

last: Manahan


title: Small RNA profiles from human genic regions suggest biogenic mechanisms and identify new Argonaute-associated species

status: Public on Jul 31 2011

city: Copenhagen E

first: Eivind

last: Valen

state: Select

address: Ole Maaloes Vej 4

department: Dep. of Biology

country: Denmark

institute: University of Copenhagen

summary: Efforts to catalogue eukaryotic transcripts have uncovered a set of species derived from the termini and exon/intron boundaries of protein-coding loci. The biogenesis pathways of these small RNAs (sRNAs) are largely unknown, but a mechanism depending on backtracking of RNA polymerase II (RNAPII) has been suggested. Moreover, the functional relevance, if any, of these sRNAs remains elusive. By sequencing 12-100nt transcripts from cells depleted of major RNA degradation enzymes as well as RNAs associated with the effector-proteins Argonaute (AGO) 1/2, we provide mechanistic models for sRNA production and utilization. We suggest that neither splice site associated (SSa)- nor transcription start site associated (TSSa)-RNAs arise from RNAPII backtracking. Instead SSa-RNAs are largely degradation products of mRNA splicing intermediates, while TSSa-RNAs likely derive from nascent RNA protected by stalled RNAPII against nucleolysis. We also reveal new AGO1/2-associated RNAs, including such derived from 3'ends of introns (5'tailed miRtrons) and from mRNA 3'UTRs. Interestingly, both appear to draw from non-canonical microRNA (miRNA) biogenesis pathways.

overall_design: 10 samples all from HeLa in three size ranges: 12-20, 18-30 and 30-100. 1 from 12-20: nuclear; 6 from 18-30: WT, nuclear, RRP40 knockdown, Ago1&2 IP, RRP40 knockdown and Ago1&2 IP, XRN1&2 knockdown; 3 from 30-100: WT, of RRP40 knockdown, XRN1&2 knockdown.

first: Torben

middle: H

last: Jensen


title: Joint analysis of microRNome and 3'-UTRome in the endometrium of rhesus monkey

status: Public on Jul 30 2011

city: Shantou

first: Zeng-Ming

last: Yang

address: 263 Daxue Road

country: China

institute: Shantou University

summary: Here we used rhesus monkey as an animal model and compared the endometrial miRNA expression profiles during early-secretory (day 15, pre-receptive) phase and mid-secretory (day 21, receptive) phase by deep sequencing. In order to facilitate the prediction of their target genes, the 3'-UTRome was also determined using tag sequencing of mRNA 3'-termini.

overall_design: Defining the microRNome and the 3'-UTRome in the endometrium of rhesus monkey.

first: Zengming

first: Jilong

last: Liu


title: Opposing roles of E2A and Id3 that orchestrate and enforce the naive T cell fate

city: La Jolla

first: Yin

middle: Chun

last: Lin

address: 9500 Gilman Drive

department: Division of Biological Sciences

institute: UCSD

summary: It is established that E2A and its antagonist, Id3, modulate developmental progression at the pre-TCR and TCR checkpoints.  Here we show at a global scale how E2A promotes commitment to the T cell lineage and how pre-TCR mediated signalling affects E2A genome-wide occupancy.  We find aberrant development of CD4 memory-like and TFH-like cells, T-B cell conjugates and, remarkably, B cell follicles in Id3-/-thymi.  We also find that Id3-/-CD4 splenocytes exhibit increased numbers of TFH-like cells.  We propose a model in which Id3 modulates the naive versus effector/memory cell fate.  Collectively, these data show how E2A acts globally to orchestrate T-lineage development and that Id3 antagonizes E2A activity beyond the pre-TCR checkpoint to enforce the naive T cell fate.

overall_design: ChIP-Seq was performed in thymocytes isolated from either untreated Rag2-/-mice (DN3 cells) or Rag2-/- mice injected with anti-CD3e antibody (DN4 cells). ChIP used antibodies against either E2A or H3K4me1.

first: Masaki

last: Miyazaki

first: Richard

last: Rivera

first: Kazuko

first: Yasutoshi

last: Agata

first: Cornelis

last: Murre


title: RNAi promotes heterochromatic silencing through replication-coupled release of RNA pol II (ChIP-seq)

status: Public on Jul 29 2011

city: Cold Spring Harbor

first: Mikel

last: Zaratiegui

state: NY

address: 1 Bungtown Rd

department: Delbruck Bldg.

institute: Cold Spring Harbor Laboratory

summary: Heterochromatin comprises tightly compacted repetitive regions of eukaryotic chromosomes. The inheritance of heterochromatin through mitosis requires RNA interference (RNAi), which guides histone modification 1 during the DNA replication phase of the cell cycle2. Here, we show that the alternating arrangement of origins of replication and non-coding RNA in pericentromeric heterochromatin results in competition between transcription and replication. Co-transcriptional RNAi releases RNA polymerase II (PolII), allowing completion of DNA replication by the leading strand DNA polymerase, and associated histone modifying enzymes3 which spread heterochromatin with the replication fork. In the absence of RNAi, stalled forks are repaired by homologous recombination without histone modification.

overall_design: RNA PolII ChIP from wild type and dcr1-deleted samples in exponentially growing and HU-arrested cultures.

first: Stephane

middle: E

last: Castel

first: Danielle

middle: V

last: Irvine

first: Anna

last: Kloc

first: Jie

last: Ren

first: Fei

last: Li

first: Elisa

last: de Castro

first: Laura

last: MarÃn

first: Ann-Yun

last: Chang

first: Derek

last: Goto

first: W

middle: Z

last: Cande

first: Francisco

last: Antequera

first: Benoit

last: Arcangioli

first: Rob

last: Martienssen


title: The tumor antigen PRAME is a substrate recognition subunit of a Cul2-based ubiquitin ligase and is associated with active NFY promoters

city: Nijmegen

last: Stunnenberg

address: Geert Grooteplein 28

department: Department of Molecular Biology (274)

institute: Radboud University

summary: The human tumor antigen PRAME (Preferentially expressed antigen of melanoma) is frequently overexpressed in tumors. High PRAME levels correlate with poor clinical outcome of several cancers, but the mechanisms by which PRAME could be involved in tumorigenesis remain largely elusive. We applied protein-complex purification strategies and identified PRAME as a substrate recognition subunit of a Cullin2-based E3 ubiquitin ligase. Genome-wide chromatin immunoprecipitation experiments revealed that PRAME is specifically enriched at NF-Y promoters that are transcriptionally active, suggesting a role in gene activation. Our results are consistent with the involvement of the PRAME ubiquitin ligase complex in NF-Y-mediated transcriptional regulation.

overall_design: ChIP-seq binding profiles of PRAME (ChIP-seq using the preimmune serum was used as negative control), NFYA, and NFYB, and expression analysis by RNA-seq in K562 human leukemia cell line

first: Adalberto

last: Costessi

first: Hendrik


title: Analysis of the Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development.

city: Storrs

first: James

last: Lindsay

state: CT

address: 354 Mansfield Road, Unit 2131

department: Molecular and Cell Biology

institute: University of Connecticut

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

overall_design: Refer to individual Series

first: Rachel

last: O'Neill


title: Small RNA from W23 maize anthers at 1mm, 1.5mm, and 2mm

status: Public on Jul 28 2011

city: Stanford

first: John

last: Fernandes

address: 385 Serra Mall

department: Bio Sci

institute: Stanford University

summary: Illumina small RNA sequence data from maize anthers at 3 stages - 1mm, 1.5mm, and 2mm.

overall_design: Plants were field-grown and then anthers dissected and grouped according to length.  RNA was extracted using TriReagent protocol.  Each of the 3 sample types were sequenced separately.

first: Guo-ling

first: Virginia

last: Walbot


title: Nucleosome maps in S. cerevisiae at varying phosphate concentrations

city: Singapore

first: Yuriy

middle: L

last: Orlov

address: 60 Biopolis Street

department: Computational Systems Biology

country: Singapore

institute: Genome Institute of Singapore

summary: Genome wide maps of nucleosome occupancy in yeast have been produced through deep sequencing of nuclease-protected DNA. These maps have been obtained from crosslinked chromatin in vivo at varying phosphate concentrations (no phoshate and 10mM phosphate concentration). Here, we analyze these maps in combination with existing TF binding data (Harbison et al., Nature, 2004, 431(7004):99-104), and with new gene expression experiments reported here (GSE26770). We also confirm previous conclusions that the intrinsic,sequence dependent binding of nucleosomes helps determine the localization of TF binding sites.

overall_design: High-throughput sequencing of yeast nucleosomal DNA at varying phosphate concentration. Yeast S. cerevisiae (strain: PHO4-MYC::TRP1; CBF1-3HA::LEU2) in log phase was grown in PNB medium with no phosphate for 3 hours and then shifted to various phosphate concentration (0mM and 10 mM) for 80 minutes. After micrococcal nuclease treatment, reverse crosslink and gel purification mononucleosome were isolated. The sequencing by Illumina Solexa following manufacturer protocol has provided mononucleosomal maps in yeast genome (Oct. 2003 SGD/sacSer1 genome release) at two phosphate concentrations (starvation and normal).

first: Jin-Quan

last: Run

first: Xiaowei

last: Xue

first: Neil

middle: D

last: Clarke


title: Tammar wallaby CENP-A ChIP-seq

summary: Chromatin immunoprecipitation from tammar wallaby pouch young cells for DNA bound to CENP-A

overall_design: Chromatin from one Tammar wallaby cell line, total of two technical replicates, 1/8th plate each, IgG and No Antibody IPs performed but not sequenced


title: Establishment of Enhancer Repertoires that Orchestrate the Myeloid and Lymphoid Cell Fates (ChIP-Seq dataset)

status: Public on Sep 01 2011

first: Yin

last: Lin

summary: Recent studies have documented genome-wide binding patterns of transcriptional regulators and their associated epigenetic marks in hematopoietic cell lineages. In order to determine how epigenetic marks are established and maintained during developmental progression, we have generated long-term cultures of hematopoietic progenitors by enforcing the expression of the E-protein antagonist Id2. Hematopoietic progenitors that express Id2 are multipotent and readily differentiate upon withdrawal of Id2 expression into committed B lineage cells, thus indicating a causative role for E2A in promoting the B cell fate. Genome-wide analyses revealed that a substantial fraction of lymphoid and myeloid enhancers are pre-marked by H3K4me1 in multipotent progenitors. However, H3K4me1 levels at a subset of enhancers are elevated during developmental progression, resulting in evolving enhancer repertoires that we propose orchestrate the myeloid and B cell fates.

overall_design:
ChIP-Seq and gene expression profiling were performed in an inducible hematopoietic pluripotent cell line that can be differentiated into multiple lymphoid lineages. This submission contains ChIP-Seq data.

Recent studies have demonstrated a tight correlation between transcriptionally active promoters and H3K4 trimethylation, whereas H3K4 monomethylation has been associated with enhancer activity. To determine whether the changes in gene expression patterns upon differentiation correlate with the presence of H3K4me3 as well as H3K4me1, ChIP-sequencing was performed on these two marks on cell lysates that were derived from Id2-HPCs and differentiated Id2-HPCs. The H3K4me1 marks were further analyzed to investigate the dynamics of enhancer repertoires between these cells. Id2-HPCs were cultured in IMDM medium supplemented with 10% FCS/2% PSG/β-me and IL7, Flt3-ligand, and SCF cytokines on S17 feeder cells in a humidified incubator at 37 degrees C with 5% CO2. Id2-HPC expanded cells were depleted of small (<1-5%) numbers of CD19-, CD25- and CD11b-positive cells by auto-MACS. For myeloid differentiation, cells were cultured for up to 6 days in IMDM medium supplemented with 10% FCS/2% PSG/β-me and IL3, Flt3L, GMCSF and MCSF cytokines. To promote B-cell differentiation, cells were cultured for up to 5 days in IMDM medium supplemented with 10% FCS/2% PSG/β-me and IL-7 and SCF cytokines on S17 feeder cells in the presence of 1 ug/mL doxycycline, or alternatively, in alpha-MEM medium in the presence of cytokines and on Tst-4 stromal cells.

first: Elinore

middle: M

last: Mercer

first: Christopher

last: Benner

first: Suchit

last: Jhunjhunwala

first: Janusz

last: Dutkowski

first: Martha

last: Flores

first: Mikael

last: Sigvardsson

first: Trey

last: Ideker

middle: K

last: Glass

first: Cornelis

last: Murre


title: RNAi promotes heterochromatic silencing through replication-coupled release of RNA pol II (superseries)

first: Mikel

last: Zaratiegui

first: Stephane

last: Castel

first: Danielle

last: Irvine

first: Anna

last: Kloc

first: Jie

last: Ren

first: Fei

last: Li

first: Elisa

last: de Castro

first: Laura

last: Marin

first: Ann-Yun

last: Chang

first: Derek

last: Goto

first: W

last: Cande

first: Francisco

last: Antequera

first: Benoit

last: Arcangioli

first: Rob

last: Martienssen


title: SuperSAGE evidence for CD14++CD16+ monocytes as a third monocyte subset

status: Public on Jul 24 2011

city: Frankfurt am Main

first: Björn

last: Rotter

country: Germany

institute: GenXPro-GmbH

summary: Monocytes are a heterogeneous cell population with subset-specific functions and phenotypes. The differential expression of CD14 and CD16 distinguishes classical CD14++CD16-, intermediate CD14++CD16+ and non-classical CD14+CD16++ monocytes. However, CD14++CD16+ monocytes remain the most poorly characterized subset so far. Therefore we analyzed the transcriptomes of the three monocyte subsets using SuperSAGE in combination with high-throughput sequencing. Analysis of 5,487,603 tags revealed unique identifiers of CD14++CD16+ monocytes, delineating these cells from the two other monocyte subsets. CD14++CD16+ monocytes were linked to antigen processing and presentation (e.g. CD74, HLA-DR, IFI30, CTSB), to inflammation and monocyte activation (e.g. TGFB1, AIF1, PTPN6), and to angiogenesis (e.g. TIE2, CD105). Therefore we provide genetic evidence for a distinct role of CD14++CD16+ monocytes in human immunity.

overall_design: Human monocyte subsets (CD14++CD16-, CD14++CD16+, CD14+CD16++) were isolated from 12 healthy volunteers based on MACS technology. Total RNA from monocyte subsets was isolated and same aliquots from each donor and monocyte subset were matched for SuperSAGE. Three SuperSAGE libraries (CD14++CD16-, CD14++CD16+ and CD14+CD16++) were generated.

first: Adam

last: Zawada

first: Kyrill

last: Rogacev

first: BjÃ¶rn

first: Peter

last: Winter

first: Rolf

middle: R

last: Marell

first: Danilo

last: Fliser

first: Gunnar

last: Heine


title: Unique small RNA signatures uncovered in the tammar wallaby genome [small RNA_seq]

first: James

last: Lindsay

summary: Small RNA isolation of miRNAs, crasiRNAs and piRNAs for RNAseq from tammar wallaby pouch young

overall_design: RNA-seq of various small RNA classes in tammar wallaby

first: Rachel

middle: J

last: O'Neill


title: RNAi promotes heterochromatic silencing through replication-coupled release of RNA pol II (RNA seq)

status: Public on Jul 21 2011

first: Mikel

last: Zaratiegui

summary: Heterochromatin comprises tightly compacted repetitive regions of eukaryotic chromosomes. The inheritance of heterochromatin through mitosis requires RNA interference (RNAi), which guides histone modification during the DNA replication phase of the cell cycle. Here, we show that the alternating arrangement of origins of replication and non-coding RNA in pericentromeric heterochromatin results in competition between transcription and replication. Co-transcriptional RNAi releases RNA polymerase II (PolII), allowing completion of DNA replication by the leading strand DNA polymerase, and associated histone modifying enzymes which spread heterochromatin with the replication fork. In the absence of RNAi, stalled forks are repaired by homologous recombination without histone modification.

overall_design: small RNA cloning from wild type and dcr1-deleted strains

first: Stephane

last: Castel

first: Danielle

last: Irvine

first: Anna

last: Kloc

first: Jie

last: Ren

first: Fei

last: Li

first: Elisa

last: de Castro

first: Laura

last: MarÃn


title: Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing

city: Augusta

first: Huidong

last: Shi

state: GA

department: Georgia Cancer Center

institute: Augusta University

type: Methylation profiling by high throughput sequencing

summary:
We applied the solution hybrid selection approach to the enrichment of CpG islands (CGIs) and promoter sequences from the human genome for targeted high-throughput bisulfite sequencing. A single lane of Illumina sequences allowed accurate and quantitative analysis of 1 million CpGs in more than 21,408 CGIs and 15,946 transcriptional regulatory regions. More than 85% of capture probes successfully yielded quantitative DNA methylation information of targeted regions.

In this study, we generated genome-wide, single-base resolution DNA methylation maps in three of the most commonly used breast cancer cell lines.Differentially methylated regions (DMRs) were identified in the 5?-end regulatory regions, as well as the intra- and intergenic regions, particularly in the X chromosome among the three cell lines. The single CpG resolution methylation maps of many known tumor suppressor genes were also established in the three cell lines.

overall_design: Here we present a novel approach that combines solution-phase hybrid selection and massively parallel bisulfite sequencing to profile DNA methylation in targeted CGI and promoter regions. We designed 51,466 single strand DNA oligonucleotides (160-mer) which target 23,441 CGIs and the transcription start sites of 19,369 known genes in the human genome. The synthetic long DNA oligonucleotides were converted into biotinylated RNA probes for solution-phase hybridization capture of target DNA. The captured genomic DNA was treated with sodium bisulfite, amplified by PCR and sequenced using Illumina GA IIx sequencer.


title: Sequencing of microRNA in spermatogonial stem cell enriched cell populations.

status: Public on Jul 20 2011

city: houston

first: Zhiyv

last: Niu

state: tx

address: One baylor plaza, 506E

department: Animal Biology

institute: University of Pennsylvania

summary: MicroRNAs (miRs) play a key role in the control of gene expression in a wide array of tissue systems where their functions include the regulation of self-renewal, cellular differentiation, proliferation, and apoptosis. However, the functional importance of individual miRs in controlling spermatogonial stem cell (SSC) homeostasis has not been investigated. Using high-throughout sequencing, we profiled the expression of miRs in the Thy1+ testis cell population, which is highly enriched for SSCs, and the Thy1- cell population, composed primarily of testis somatic cells. In addition, we profiled the global expression of miRs in cultured germ cells, also enriched for SSCs. Our results demonstrate that miR-21, along with miR-34c, -182, -183, -146a, -465a-3p, -465b-3p, -465c-3p, and -465c-5p are preferentially expressed in the Thy1+ SSC-enriched population, as compared to Thy1- somatic cells, and we further observed that Thy1+ SSC-enriched testis cells and SSC-enriched cultured germ cells share remarkably similar miR expression profiles.

overall_design: Spermatogonial Stem Cell enriched cell populations (freshly isolated and short-term cultured) and somatic cell populations were isolated from C57B/L6 mouse donors and subjected to small RNA isolation and sequencing.

first: Ralph

last: Brinster


title: Transcriptome analysis of Cymelarsan resistant and Cymelarsan sensitive strains of Trypanosoma brucei.

city: Glasgow

first: Anneli

last: Cooper

address: GBRC, 120 University Place

department: Wellcome Centre for Molecular Parasitology

country: United Kingdom

institute: University of Glasgow

summary: A drug sensitive stock of T.b.brucei (STIB247) was used to generate a drug resistant strain (247MelCyR), expressing  130-fold increase in resistance to the melaminophenyl arsenical Cymelarsan (MelCy) by subcurative treatment in mice. Expression of the Cymelarsan resistant phenotype was maintained in 247MelCyR following adaptation to procyclic form in vitro culture. Here we have compared the transcriptomes of the STIB247 and 247MelCyR strains from procyclic cell culture, using digital gene expression (DGE) analysis.

overall_design: Digital gene expression analysis was performed on RNA derived from 2 biological replicates each of Cymelarsan resistant (247MelCyR) and Cymelarsan sensitive (STIB 247), T.b.brucei procyclic cell culture.

first: Caroline

last: Clucas

first: Paul

last: Johnson

first: Annette

last: MacLeod

first: Andrew

last: Tait

first: C

last: Turner


title: The Genetic Basis of Rapidly Evolving Male Genital Morphology in Drosophila

status: Public on Jul 22 2011

first: Sudeep

last: Srivastava

address: 1050 Childs Way

summary: Deep sequencing of total RNA extracted from the genital discs of males for each of the following strains : Drosophila sechellia, Drosophila mauritiana, hybrid introgression line 3Q1(A) and hybrid introgression line Q1(A)

sample_organism: Drosophila sechellia x Drosophila mauritiana

overall_design: Analysis of poly(A)+ RNA for three independent biological replicates of sequencing libraries for each of the following strains: D. sechellia w, D. mauritiana P-insertion Q1, hybrid introgression line 3Q1(A), and hybrid introgression line Q1(A).  Male genital discs were obtained as described above, and total RNA was extracted using RNAqueousÂ®-Micro Kit (Ambion).  Poly(A)+ transcripts were isolated subsequently using MicroPoly(A)Puristâ¢ Kit (Ambion).  To facilitate normalization of reads across our samples, at this stage of library construction we spiked-in small amounts of exogenous RNA from ArrayControlâ¢ Kit (Ambion) into each sample of poly(A)+ RNA. Paired-end sequencing was carried out by loading the samples onto four lanes (three samples per lane) of a flow cell and run on an Illumina Genome Analyzer IIx sequencer using 72 cycles per end of each paired-end read.  Biological replicates of each genotype were loaded onto separate lanes.

first: J

last: Masly

last: Dalton

first: S

first: L

last: Chen

first: M

middle: N

last: Arbeitman


title: The human mitochondrial transcriptome

city: Sydney

first: Tim

middle: R.

last: Mercer

state: New South Wales

address: 384 Victoria Street Darlinghurst NSW 2010

country: Australia

institute: Garvan

summary: The human mitochondrial genome comprises a distinct genetic system transcribed as precursor polycistronic transcripts that are subsequently cleaved to generate individual mRNAs, tRNAs and rRNAs. Here we provide a comprehensive analysis of the human mitochondrial transcriptome across multiple cell lines and tissues. Using directional deep sequencing and parallel analysis of RNA ends, we demonstrate wide variation in mitochondrial transcript abundance, and precisely resolve transcript processing and maturation events. We identify novel transcripts, including small RNAs, and observe the enrichment of several nuclear RNAs in mitochondria. Using high-throughput in vivo DNaseI footprinting, we establish the global profile of DNA-binding protein occupancy across the mitochondrial genome at single nucleotide resolution, revealing novel regulatory features at mitochondrial transcription initiation sites and functional insights into disease-associated variants. Together, this integrated analysis of the mitochondrial transcriptome reveals unexpected complexity in the regulation, expression, and processing of mitochondrial RNA, and itÂ  provides a resource for the future study of mitochondrial function (accessed at mitochondria.matticklab.com).

overall_design: Examination of the mitochondiral transcriptome by long and small RNA sequencing, PARE sequencing and DNAseI hypersensitivity mapping.

first: John

last: Mattick


title: Genome-wide nucleosome position maps in Saccharomyces cerevisiae

city: Bethesda

first: David

middle: Johannes

last: Clark

address: 6 Center Drive Bldg 6A Rm 2A02

department: DDB

institute: NICHD, NIH

summary: Paired-end sequencing study of nucleosomal DNA prepared from budding yeast by micrococcal nuclease digestion.

overall_design: Comparison of control cells with cells treated with 10 mM 3-aminotriazole for 20 minutes

first: Hope

middle: A

last: Cole

first: Bruce

last: Howard


title: Genome-Wide Progesterone Receptor Binding: Cell Type-Specific and Shared Mechanisms in Uterine Fibroids and Breast Cancer

status: Public on Jul 23 2011

city: Basel

first: Damian

last: Roqueiro

address: Mattenstrasse 26

department: Biosystems Science and Engineering

country: Switzerland

institute: ETH Zurich

first: Bulun

last: Serdar

first: Frasor

last: Jonna


title: Expression data from colonic biopsy samples of infliximab treated UC patients

city: Spring House

first: K

last: Li

state: PA

address: 1400 McKean Road

institute: Janssen R&D

summary:
A gene expression profiling sub-study was conducted in which colonic biopsy samples were collected for RNA extraction and hybridization to microarrays from 48 patients with UC who were participating in ACT 1, a placebo-controlled study of infliximab. Gene expression profiles from infliximab responders were compared with those of baseline and infliximab non-responder samples.
Infliximab had a significant effect on mRNA expression in treatment responders, with both infliximab dose and duration of treatment having an effect.  Genes affected are primarily involved with inflammatory response, cell-mediated immune responses, and cell-to-cell signaling. Infliximab non-responders had a molecular phenotype that closely resembled that of untreated patients with UC.  Unlike responders, non-responders do not effectively modulate TH1, TH2, and TH17 pathways.   Gene expression can differentiate placebo and infliximab responders.

overall_design: Patients with moderate-to-severe, active UC were treated with infliximab or placebo at weeks 0, 2, 6 and every 8 weeks thereafter.  Biopsy samples (n=113) were collected from 48 patients at baseline, weeks 8 and 30 for RNA extraction and microarray analysis.

first: Gary

last: Toedter

first: Katherine

first: Colleen

last: Marano

first: Keying

last: Ma

first: Sarah

last: Sague

middle: C

last: Huang

first: Xiao-Yu

last: Song

first: Paul

last: Rutgeerts

first: Frédéric

last: Baribaud


title: Allele specific mRNA-seq expression profiling in Arabidopsis thaliana Col and Ler reciprocal F1 hybrid embryo and endosperm

status: Public on Jul 18 2011

city: Cambridge

first: Mary

last: Gehring

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: High throughput Illumina sequencing of poly-A selected RNA from Arabidopsis Col and Ler reciprocal F1 hybrid embryo and endosperm tissue isolated at 6-7 days after pollination to identify imprinted genes.

overall_design: Examination of parent-of-origin specific and total gene expression in seed tissues.

first: Steven

last: Henikoff


title: Super Elongation Complex (SEC) and global genomic analyses in murine embryonic stem (ES) cells and in human cells in response to activation signals.

status: Public on Jul 19 2011

city: Kansas CIty

first: Alexander

middle: (Garrett)

last: Garruss

state: Missouri

address: 1000 East 50th Street

institute: Stowers Institute for Medical Research

summary: Transcriptional regulation of developmentally controlled genes is at the heart of differentiation and organogenesis. In this study, we have performed global genomic analyses in murine embryonic stem (ES) cells and in human cells in response to activation signals. We have identified an essential role for the ELL/P-TEFbcontaining Super Elongation Complex (SEC) in the regulation of gene expression including several genes bearing paused RNA polymerase II (Pol II). Paused Pol II has been proposed to be associated with loci that respond rapidly to environmental stimuli. However, our studies in ES cells have also identified a requirement for SEC at genes without preloaded Pol II, which also respond dynamically to differentiation signals. Our findings suggest that SEC is a major class of active P-TEFb-containing complexes required for transcriptional activation in response to environmental cues such as differentiation signals.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Examination of ELL2, AFF4, and Pol II before and after activation signals in two cell types.

first: Chengqi

last: Lin

middle: S

last: Garrett

first: Ali

last: Shilatifard


title: Multiple platform assessment of the EGF dependent transcriptome by microarray and deep tag sequencing analysis

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

institute: IGTP

type: Genome variation profiling by genome tiling array

summary:
Epidermal growth factor (EGF) is a key regulatory growth factor activating a myriad of processes affecting cell proliferation and survival that are relevant to normal development and disease. Here we have used a combined approach to study the EGF dependent transcriptome of HeLa cells. We obtained mRNA expression profiles using multiple long oligonucleotide based microarray platforms (from Agilent, Operon, Febit, and Illumina) in combination with digital gene expression profiling (DGE) with the Illumina Genome Analyzer I (GA-I). By applying a procedure for cross-platform data meta-analysis based on rank product and global ancova tests, we establish a well validated gene set with transcript levels altered after EGF treatment. We used this robust gene list to build higher order networks of gene interaction by interconnecting associated networks, supporting and extending the important role of the EGF signaling pathway in cancer. In addition, we found a whole new set of genes previously unrelated to the currently accepted EGF associated cellular functions, among which are metallothionein genes. We propose the use of global genomic cross-validation to generate more reliable datasets derived from high content technologies (microarrays or deep sequencing). This approach should help to improve the confidence of downstream in silico functional inference analyses based on high content data.

Keywords: treated vs. untreated comparison, time course

overall_design:
Time course experiment comparing HeLa gene expression in response to EGF analyzed on different microarray platforms (Agilent, IMPPC, Illumina, and Operon) and by digital gene expression using short read high throughput tag sequencing. Three independent experiments were performed where HeLa cells were serum deprived for 24 hours and were either left untreated or treated with EGF for 6, and 24 h and harvested for RNA extraction. Technical dye swap duplicates were performed for each of the three biological replicates in both time points.

Comparative genomic hybridization of HeLa cell genomic DNA versus  poooled genomic DNA from blood obtained from human females conducted on commercial oligonucleotide microarrays (Human Genome CGH Microarray Kit 244A, Agilent Technologies) in order to assess DNA dosage dependence of gene expression levels and response to EGF.

Digital gene expression using short read high throughput tag sequencing data submitted to NCBI's SRA

first: Franc

last: Llorens

first: Manuela

last: Hummel

first: Xavier

last: Pastor

first: Anna

last: Ferrer

first: Ana

last: Mosquera

first: Susana

last: Iraola

first: Eva

last: Gonzalez

first: Juanjo

last: Lozano


title: Genome-Wide Analysis of Host-Chromosome Binding Sites for Epstein-Barr Virus Nuclear Antigen 1 (EBNA1)

status: Public on Jul 16 2011

city: Philadelphia

first: Priyankara

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: The Epstein-Barr Virus (EBV) Nuclear Antigen 1 (EBNA1) protein is required for the establishment of EBV latent infection in proliferating B-lymphocytes.  EBNA1 is a multifunctional DNA-binding protein that stimulates DNA replication at the viral origin of plasmid replication (OriP), regulates transcription of viral and cellular genes, and tethers the viral episome to the cellular chromosome.  EBNA1 also provides a survival function to B-lymphocytes, potentially through its ability to alter cellular gene expression. Chromatin-immunoprecipitation (ChIP) combined with massively parallel deep-sequencing (ChIP-Seq) was used to identify cellular sites bound by EBNA1.  Sites identified by ChIP-Seq were validated by conventional real-time PCR, and ChIP-Seq provided quantitative, high-resolution detection of the known EBNA1 binding sites on the EBV genome at OriP and Qp.  We identified at least one cluster of unusually high-affinity EBNA1 binding sites on chromosome 11, between the divergent FAM55D and FAM55B genes.  A consensus for all cellular EBNA1 binding sites is distinct from those derived from the known viral binding sites, suggesting that some of these sites are indirectly bound by EBNA1. We conclude that EBNA1 can interact with a large number of cellular genes and chromosomal loci in latently infected cells, but that these sites are likely to represent a complex ensemble of direct and indirect EBNA1 binding sites.

overall_design: Study of Epstein-Barr virus (EBV)

first: Fang

last: Lu

last: Wikramasinghe

first: Julie

last: Norseen

first: Kevin

last: Tsai

first: Pu

last: Wang

first: Louise

last: Showe

first: Ramana

last: Davuluri

last: Lieberman


title: Splicing enhances recruitment of methyltransferase HYPB/Setd2 and methylation of histone H3 lysine 36

status: Public on Jul 25 2011

city: Marseille

first: Romain

last: Fenouil

address: Parc Scientifique et Technologique de Luminy - Case 906

department: CIML

country: France

institute: CNRS

summary: Several lines of recent evidence support a role for chromatin in splicing regulation. Here we show that splicing can also contribute to histone modification, which implies a bidirectional communication between epigenetics and RNA processing. Genome-wide analysis of histone methylation in human cell lines and mouse primary T cells reveals that intron-containing genes are preferentially marked with H3K36me3 relative to intronless genes. In intron-containing genes, H3K36me3 marking is proportional to transcriptional activity, whereas in intronless genes H3K36me3 is always detected at much lower levels. Furthermore, splicing inhibition impairs recruitment of H3K36 methyltransferase HYPB/Setd2 and reduces H3K36me3, whereas splicing activation has the opposite effect. Moreover, the increase of H3K36me3 correlates with the length of the first intron, consistent with the view that splicing enhances H3 methylation. We propose that splicing is mechanistically coupled to recruitment of HYPB/Setd2 to elongating RNA Polymerase II.

overall_design:
This experiment proposes to profile genome-wide binding profiles by ChIP-seq (Illumina, 36 bp tags) of RNA polymerase II (one biological replicate), the histone modification H3K36me3 (2 replicates) and a reference control input sample (genomic DNA after reverse cross-link, one replicate) in a human H1299 lung carcinoma cell line

*** Raw data not provided for Samples GSM766322-GSM766324.

first: SÃ©rgio

last: de Almeida

last: Grosso

first: Frederic

last: Koch

first: Silvia

last: Carvalho

first: Jorge

last: Andrade

first: Helena

last: Levezinho

first: Marta

last: Gut

first: Dirk

last: Eick

first: Ivo

first: Jean-Christophe

last: Andrau

first: Pierre

last: Ferrier

first: Maria

last: Carmo-Fonseca


title: SMAD1/5 binding regions of human pulmonary arterial smooth muscle cells (PASMCs) treated with BMP

city: Tokyo

first: Daizo

last: Koinuma

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

department: Pathology

country: Japan

institute: University of Tokyo

summary: Smad1/5 are transcription factors that engage in BMP-induced transcription. We determined and analyzed Smad1/5 binding sites by ChIP-sequencing. We used expression microarrays to compare the Smad1/5 binding sites identified by ChIP-seq to BMP-induced gene expressions.

overall_design: PASMCs were treated with BMP for 1.5 h, and anti-SMAD1/5 ChIP-seq analyses were performed using the Illumina Genome Analyzer II.

first: Masato

last: Morikawa

first: Shuichi

last: Tsutsumi

first: Eleftheria

last: Vasilaki

first: Carl-Henrik

last: Heldin

first: Hiroyuki

last: Aburatani

first: Kohei

last: Miyazono


title: An EMT-driven alternative splicing program occurs in human breast cancer and modulates cellular phenotype.

status: Public on Jul 15 2011

first: Albert

middle: W

last: Cheng

address: Room 453, 9 Cambridge Center

institute: Whitehead Institute

summary: Regulation of cell-cell junction formation and regulation of cell migration were enriched among EMT (Epithelial-Mesenchymal Transition)-associated alternatively splicing events. Our analysis suggested that most EMT-associated alternative splicing events are regulated by one or more members of the RBFOX, MBNL, CELF, hnRNP or ESRP classes of splicing factors. The EMT alternative splicing signature was confirmed in human breast cancer cell lines, which could be classified into basal and luminal subtypes based exclusively on their EMTassociated splicing pattern. Expression of EMT-associated alternative mRNA transcripts was also observed in primary breast cancer samples, indicating that EMT-dependent splicing changes occur commonly in human tumors. The functional significance of EMT-associated alternative splicing was tested by expression of the epithelial-specific splicing factor ESRP1 or depletion of RBFOX2 in mesenchymal cells, both of which elicited significant changes in cell morphology and motility towards an epithelial phenotype, suggesting that splicing regulation alone can drive critical aspects of EMT-associated phenotypic changes. The molecular description obtained here may aid in the development of new diagnostic and prognostic markers for analysis of breast cancer progression.

overall_design: Examination of transcriptomes of HMLE/Twist-ER before and after induction of EMT by tamoxifen

first: Irina

last: Shapiro

first: Christopher

middle: B

last: Burge

first: Frank

last: Gertler


title: SMAD1/5 binding regions of human umbilical vein endothelial cells (HUVECs) treated with BMP.

summary: Smad1/5 binding regions were identified by ChIP-seq.

overall_design: HUVECs were treated with BMP for 1.5 h and anti-SMAD1/5 ChIP-seq analyses were performed using Illumina genome analyzer.


title: [E-MTAB-706] Quantitative RNA-seq analysis of the transcriptome of Campylobacter jejuni

status: Public on Jul 14 2011

city: Hinxton

first: ArrayExpress

last: EBI

state: Cambridgeshire

address: Wellcome Trust Genome Campus

institute: European Bioinformatics Institute

summary:
RNA-seq analysis of the transcriptome of wild type C.jejuni NCTC11168, and of an rpoN mutant of the same strain, both grown in vitro.

ArrayExpress Release Date: 2011-06-14

Publication Title: Quantitative RNA-seq analysis of the transcriptome of Campylobacter jejuni
Publication Author List: Roy R. Chaudhuri, Lu Yu, Alpa Kanji, Timothy T. Perkins, Paul P. Gardner, Jyoti Choudhary, Duncan J. Maskell, Andrew J. Grant

Person Roles:  submitter
Person Last Name: Chaudhuri
Person First Name: Roy
Person Mid Initials: R
Person Email: roy.chaudhuri@gmail.com
Person Phone: 441000000000
Person Address: Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, United Kingdom
Person Affiliation: University of Cambridge

overall_design:
Experimental Design: genetic_modification_design
Experimental Design: in_vitro_design
Experimental Design: co-expression_design
Experimental Factor Name: GENOTYPE
Experimental Factor Type: genotype


title: Transcriptomes of Frankia sp. strain CcI3 in growth transitions

city: Beltsville

first: Derek

middle: Martens

last: Bickhart

address: Building 005, Rm 318, BARC-West 10300 Baltimore Ave

department: BARC

institute: USDA ARS

summary: Background: Frankia sp. strains are actinobacteria that form N2-fixing root nodules on angiosperms. Several reference genome sequences are available enabling transcriptome studies in Frankia sp.  Genomes from Frankia sp. strains differ markedly in size, a consequence proposed to be associated with a high number of indigenous transposases, more than 200 of which are found in Frankia sp. strain CcI3 used in this study.  Because Frankia exhibits a high degree of cell heterogeneity as a consequence of its mycelial growth pattern, its transcriptome is likely to be quite sensitive to culture age.  This study focuses on the behavior of the Frankia sp. strain CcI3 transcriptome as a function of nitrogen source and culture age.   Results:  To study global transcription in Frankia sp. CcI3 grown under different conditions, complete transcriptomes were determined using high throughput RNA deep sequencing.  Samples varied by time (five days vs. three days) and by culture conditions (NH4+ added vs. N2 fixing). Assembly of millions of reads revealed more diversity of gene expression between five-day and three-day old cultures than between three day old cultures differing in nitrogen sources.  Heat map analysis organized genes into groups that were expressed or repressed under the various conditions compared to median expression values.  Twenty-one SNPs common to all three transcriptome samples were detected indicating culture heterogeneity in this slow-growing organism.  Significantly higher expression of transposase ORFs was found in the five-day and N2-fixing cultures, suggesting that N starvation and culture aging provide conditions for on-going genome modification. Transposases have previously been proposed to participate in the creating the large number of gene duplication or deletion in host strains. Subsequent RT-qPCR experiments confirmed predicted elevated transposase expression levels indicated by the mRNA-seq data.  Conclusions:  The overall pattern of gene expression in aging cultures of CcI3 suggests significant cell heterogeneity even during normal growth on ammonia.  The detection of abundant transcription of nif (nitrogen fixation) genes likely reflects the presence of anaerobic, N-depleted microsites in the growing mycelium of the culture, and the presence of significantly elevated transposase transcription during starvation indicates the continuing evolution of the Frankia sp. strain CcI3 genome, even in culture, especially under stressed conditions.  These studies also sound a cautionary note when comparing the transcriptomes of Frankia grown in root nodules, where cell heterogeneity would be expected to be quite high.

overall_design: Detection of gene expression variance among Frankia HfpCci3 (Cci3) cells grown in ammonium chloride for three days, five days and HfpCci3 cells grown in nitrogen fixing conditions for three days using mRNA-seq

first: David

last: Benson


title: Dynamic transcriptional events in embryonic stem cells mediated by the super elongation complex (SEC).

first: Alexander

last: Garruss

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

overall_design: Refer to individual Series


title: SMAD1/5 binding regions and expression data of human umbilical vein endothelial cells (HUVECs) and pulmonary arterial smooth muscle cells (PASMCs) treated with BMPs


title: Gene expression of polyoma middle T antigen induced mammary tumors

city: Rockville

first: Ying

last: Hu

email: yhu@mail.nih.gov, hunterk@mail.nih.gov

address: 9609 Medical Center Dr.

department: NCI/CCR

institute: NIH

first: Kent

last: Hunter


title: Zelda binding in the early Drosophila melanogaster embryo marks regions subsequently activated at the maternal-to-zygotic transition

city: Jerusalem

first: Tommy

last: Kaplan

address: Givat Ram Campus

department: School of Computer Science and Engineering

country: Israel

institute: Hebrew University

summary: The earliest stages of development in most metazoans are driven by maternally deposited proteins and mRNAs, with widespread transcriptional activation of the zygotic genome occurring hours after fertilization, at a period known as the maternal-to-zygotic transition (MZT). In Drosophila, the MZT is preceded by the transcription of a small number of genes that initiate sex determination, patterning and other essential developmental processes. The zinc-finger transcription factor Zelda (ZLD) plays a key role in the transcriptional activation of these earliest-expressed genes. To better understand the mechanisms of ZLD activation and the range of its targets, we used chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq) to map regions bound by ZLD prior to (mitotic cycles 8 and 9), during (mitotic cycles 13 and early 14) and after (late mitotic cycle 14) the MZT. Although only a handful of genes are transcribed prior to mitotic cycle 10, we identified thousands of regions bound by ZLD in cycle 8-9 embryos, most of which remain bound through mitotic cycle 14. As expected, these ZLD-bound regions include the promoters and enhancers of the small subset of genes transcribed at this early stage. However we also observed ZLD bound at cycle 8-9 to the promoters of a large fraction of the several thousand genes whose first transcription does not occur until roughly an hour and four mitotic cycles later. These early ZLD-bound regions include virtually all of the thousands of known and presumed enhancers bound at cycle 14 by the transcription factors that regulate patterned gene activation during the MZT. The association between early ZLD binding and MZT activity is so strong that ZLD binding alone can be used to identify active promoters and regulatory sequences with high specificity and selectivity. This strong early association of ZLD with regions not active until the MZT suggests that ZLD is not only required for the earliest wave of transcription, but also plays a major role in activating the genome at the MZT.

overall_design: Genome-wide mapping of Zelda in wild-type Drosophila melanogaster embryos prior (mitotic cycles 8-9), during (cycles 13-14), and after (late cycle 14) maternal-to-zygotic transition

first: Melissa

last: Harrison

first: Xiao-Yong

last: Li

first: Michael

last: Botchan

last: Eisen


title: [E-MTAB-636] Plasmodium yoelii RNA-Seq

summary:
Plasmodium yoelii YM asexual blood stage parasites express multiple members of the py235 gene family, part of the super-family of genes including those coding for Plasmodium vivax reticulocyte binding proteins and Plasmodium falciparum RH proteins. Dr Tony Holder's laboratory (NIMR, London) has been successful in deleting one of the RH family genes (Py01365) by transfection and insertion of the TgDHFR gene, and cloned the resulting parasite in YM background. The gene expression patterns of the mutant parasite line were compared to that of the wild type YM parasite.

ArrayExpress Release Date: 2011-04-25

Publication Title: Targeted Disruption of py235ebp-1: Invasion of Erythrocytes by Plasmodium yoelii Using an Alternative Py235 Erythrocyte Binding Protein
Publication Author List: Solabomi A. Ogun, Rita Tewari, Thomas D. Otto, Steven A. Howell, Ellen Knuepfer, Deirdre A. Cunningham, Zhengyao Xu, Arnab Pain, Anthony A. Holder

Person Roles:  submitter
Person Last Name: Service
Person First Name: Submission
Person Mid Initials:
Person Email: datahose@sanger.ac.uk
Person Phone:
Person Address: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom
Person Affiliation: Wellcome Trust Sanger Institute

Person Roles:  investigator
Person Last Name: Holder
Person First Name: Anthony
Person Mid Initials: A
Person Email: aholder@nimr.mrc.ac.uk
Person Phone:
Person Address: Division of Parasitology, MRC National Institute for Medical Research, London, UK
Person Affiliation: MRC National Institute for Medical Research

Person Roles:  Project Coordinator
Person Last Name: Sanders
Person First Name: Mandy
Person Mid Initials: J
Person Email: mjs@sanger.ac.uk
Person Phone: 01223 834244
Person Address: Wellcome Trust Genome Campus,Hinxton,Cambridge. CB10 1SA UK
Person Affiliation: Wellcome Trust Sanger Institute

overall_design:
Experimental Design: genetic_modification_design
Experimental Design: in_vivo_design
Experimental Design: co-expression_design
Experimental Factor Name: GENETICMODIFICATION
Experimental Factor Name: GENOTYPE
Experimental Factor Type: genetic_modification
Experimental Factor Type: genotype


title: [E-MTAB-612] GENCODE PCR-Seq Batch I

summary:
As part of the ENCODE consortium the GENCODE project is producing a reference gene set through manual and automated gene prediction. Selected transcript models are verified experimentally by RT-PCR amplification followed by sequencing. This is the RNASeq part of batch I, based on annotation from July 2008 (without pseudogenes).

ArrayExpress Release Date: 2011-05-01

Publication Title: GENCODE: producing a reference annotation for ENCODE
Publication Author List: Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R, Swarbreck D, Rossier C, Ucla C, Hubbard T, Antonarakis SE, Guigo R

Person Roles:  submitter
Person Last Name: Kokocinski
Person First Name: Felix
Person Mid Initials:
Person Email: fsk@sanger.ac.uk
Person Phone: -498006
Person Address: Wellcome Trust Genome Campus, Hinxton, UK
Person Affiliation: Wellcome Trust Sanger Institute

Person Roles:  investigator
Person Last Name: Hubbard
Person First Name: Tim
Person Mid Initials:
Person Email: th@sanger.ac.uk
Person Phone: -498055
Person Address: Wellcome Trust Genome Campus, Hinxton, UK
Person Affiliation: Wellcome Trust Sanger Institute

Person Roles:  investigator
Person Last Name: Reymond
Person First Name: Alexandre
Person Mid Initials:
Person Email: Alexandre.Reymond@unil.ch
Person Phone:
Person Address: Lausanne, Switzerland
Person Affiliation: University of Lausanne

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

overall_design:
Experimental Design: co-expression_design
Experimental Design: high_throughput_sequencing_design
Experimental Design: organism_part_comparison_design
Experimental Factor Name: ORGANISM_PART
Experimental Factor Type: organism_part


title: [E-MTAB-610] Tag profiling of genes from two Pachycladon species

summary:
Tag profiling and expression analysis of genes from Pachycladon enysii and Pachycladon fastigiatum.

ArrayExpress Release Date: 2011-06-01

Publication Title: Short read expression profiling in a non-model allopolyploid plant
Publication Author List: Voelckel, C, Gruenheit, N, Biggs, P,  Deusch, O, Lockhart, PJ

Person Roles:  submitter
Person Last Name: Voelckel
Person First Name: Claudia
Person Mid Initials:
Person Email: c.voelckel@massey.ac.nz
Person Phone:
Person Address: Institute of Molecular Biosciences, Private Bag 11 222, Palmerston North 4442
Person Affiliation: Institute of Molecular Biosciences, Allan Wilson Centre for Molecular Ecology and Evolution

sample_organism:
Pachycladon fastigiatum
Pachycladon enysii

overall_design:
Experimental Design: differential_expression_design
Experimental Factor Name: Population
Experimental Factor Type: Population
Quality Control Type: technical_replicate


title: [E-MTAB-587] PCR_artifacts

summary:
WARNING: This library was yield low amount of material and it was over-amplified by PCR. This libraries are used study the robustness of several statitical methods against PCR artifacts. ChIP experiments were performed on Arabidopsis wildtype inflorescences using an antibody raised against a C-terminal peptide of SEP3.

ArrayExpress Release Date: 2011-04-27

Publication Title: ChIP-seq Analysis in R (CSAR): An R package for the statistical detection of protein-bound genomic regions
Publication Author List: Jose M. Muino, Kerstin Kaufmann, Roeland C. H. J. van Ham, Gerco C. Angenent, and Pawel Krajewski

Person Roles:  submitter
Person Last Name: Muino
Person First Name: Jose
Person Mid Initials: M.
Person Email: jose.muino@wur.nl
Person Phone: 0317-481122
Person Address: Droevendaalsesteeg 1, P.O. Box 16, 6700 AA Wageningen, The Netherlands
Person Affiliation: Plant Research International B.V.

overall_design:
Experimental Design: development_or_differentiation_design
Experimental Design: in_vivo_design
Experimental Design: ChiP-seq
Experimental Factor Name: CHIP-ANTIBODY
Experimental Factor Name: PCR_amplification
Experimental Factor Type: Chip-antibody
Experimental Factor Type: PCR_amplification


title: [E-MTAB-552] Transcriptome Analysis of the potato (genotype RH89-039-16)

summary:
Transcription profiling by high throughput sequencing of the potato (genotype RH89-039-16)

ArrayExpress Release Date: 2011-07-11

Person Roles:  submitter
Person Last Name: Soenderkaer
Person First Name: Mads
Person Mid Initials:
Person Email: mson@bio.aau.dk
Person Phone: 4530532492
Person Address: Sohngaardsholmsvej 49, 9000 Aalborg, Denmark
Person Affiliation: Aalborg University

overall_design:
Experimental Design: cell_type_comparison_design
Experimental Design: in_vivo_design
Experimental Design: co-expression_design
Experimental Factor Name: ORGANISMPART
Experimental Factor Name: GROWTHCONDITION
Experimental Factor Name: DEVELOPMENTALSTAGE
Experimental Factor Type: organism_part
Experimental Factor Type: growth_condition
Experimental Factor Type: developmental_stage


title: [E-MTAB-550] Toxoplasma gondii RNASeq

summary:
Recent advances in high throughput sequencing methodologies allow the opportunity to probe in depth the transcriptomes of organisms including N. caninum and Toxoplasma gondii. In this project, we are using Illumina sequencing technology to analyze the transcriptome (RNA-Seq) of experimentally accessible stages (e.g. tachyzoites at different times points) of T. gondii VEG strain. The aim is to make comparative transcriptional landscape maps of Neospora and Toxoplasma at different time points at different life cycle stages and compare levels of expression of orthologous genes in these two organisms.

ArrayExpress Release Date: 2011-02-08

Person Roles:  submitter
Person Last Name: Service
Person First Name: Submission
Person Mid Initials:
Person Email: datahose@sanger.ac.uk
Person Phone:
Person Address: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom
Person Affiliation: Wellcome Trust Sanger Institute

Person Roles:  Investigator
Person Last Name: Reid
Person First Name: Adam
Person Mid Initials:
Person Email: ar11@sanger.ac.uk
Person Phone: 01223 834244
Person Address: Wellcome Trust Genome Campus,Hinxton,Cambridge. CB10 1SA UK
Person Affiliation: Wellcome Trust Sanger Institute

Person Roles:  Project Coordinator
Person Last Name: Sanders
Person First Name: Mandy
Person Mid Initials: J
Person Email: mjs@sanger.ac.uk
Person Phone: 01223 834244
Person Address: Wellcome Trust Genome Campus,Hinxton,Cambridge. CB10 1SA UK
Person Affiliation: Wellcome Trust Sanger Institute

overall_design:
Experimental Design: development_or_differentiation_design
Experimental Design: cell_line_design
Experimental Design: in_vitro_design
Experimental Design: co-expression_design
Experimental Factor Name: DevelopmentalStage
Experimental Factor Name: CellLine
Experimental Factor Type: developmental stage
Experimental Factor Type: cell_line


title: [E-MTAB-502] Citrobacter rodentium transcriptomics (Regulation)

summary:
Whole genome trancription study of Citrobacter rodentium grown in rich media.

Publication Title: Citrobacter rodentium is an Unstable Pathogen Showing Evidence of Significant Genomic Flux
Publication Author List: Nicola K. Petty, Theresa Feltwell, Derek Pickard, Simon Clare, Ana L. Toribio, Maria Fookes, Kevin Roberts, Rita Monson, Satheesh Nair, Robert A. Kingsley, Richard Bulgin, Siouxsie Wiles, David Goulding, Craig Corton, Nicola Lennard, David Harris, David Willey, Richard Rance, Lu Yu, Jyoti S. Choudhary, Carol Churcher, Michael A. Quail, Julian Parkhill, Gad Frankel, Gordon Dougan, George P.C. Salmond, Nicholas R. Thomson

ArrayExpress Release Date: 2011-02-12

Person Roles: investigator
Person Last Name: Thomson
Person First Name: Nicholas
Person Mid Initials:
Person Email: nrt@sanger.ac.uk
Person Phone:
Person Address: Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Person Affiliation: Wellcome Trust Sanger Institute

Person Roles: submitter
Person Last Name: Service
Person First Name: Submission
Person Mid Initials:
Person Email: datahose@sanger.ac.uk
Person Phone:
Person Address: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom
Person Affiliation: Wellcome Trust Sanger Institute

overall_design:
Experimental Design: individual_genetic_characteristics_design
Experimental Design: in_vitro_design
Experimental Design: co-expression_design
Experimental Factor Name: GENOTYPE
Experimental Factor Type: genotype


title: [E-MTAB-549] Neospora caninum RNAseq

summary:
Recent advances in high throughput sequencing methodologies allow the opportunity to probe in depth the transcriptomes of organisms including N. caninum. In this project, we are using Illumina sequencing technology to analyze the transcriptome (RNA-Seq) of experimentally accessible stages (e.g. tachyzoites at different times points) of N. caninum NCLiv. The aim is to make transcriptional landscape maps at different time points at different life cycle stages of N. caninum and compare it with equivalent datasets from the closely related parasite Toxoplasma gondii.

ArrayExpress Release Date: 2011-02-08

Person Roles:  submitter
Person Last Name: Service
Person First Name: Submission
Person Mid Initials:
Person Email: datahose@sanger.ac.uk
Person Phone:
Person Address: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom
Person Affiliation: Wellcome Trust Sanger Institute

Person Roles:  Investigator
Person Last Name: Reid
Person First Name: Adam
Person Mid Initials:
Person Email: ar11@sanger.ac.uk
Person Phone: 01223 834244
Person Address: Wellcome Trust Genome Campus,Hinxton,Cambridge. CB10 1SA UK
Person Affiliation: Wellcome Trust Sanger Institute

Person Roles:  Project Coordinator
Person Last Name: Sanders
Person First Name: Mandy
Person Mid Initials: J
Person Email: mjs@sanger.ac.uk
Person Phone: 01223 834244
Person Address: Wellcome Trust Genome Campus,Hinxton,Cambridge. CB10 1SA UK
Person Affiliation: Wellcome Trust Sanger Institute

overall_design:
Experimental Design: development_or_differentiation_design
Experimental Design: in_vitro_design
Experimental Design: co-expression_design
Experimental Factor Name: DevelopmentalStage
Experimental Factor Type: DevelopmentalStage
Quality Control Type: biological_replicate


title: Determination of transcript abundance before and after serum induction in human HCT-116 colon cancer cell line.

summary: Transcriptional regulation of developmentally controlled genes is at the heart of differentiation and organogenesis. In this study, we have performed mRNA transcript abdundance analyses in human cells in response to serum activation signal by RNA-seq.

overall_design: mRNA transcript abundance determined before and after serum activation signals using two biological replicates.

first: Chengqi

last: Lin

last: Garrett

first: Ali

last: Shilatifard


title: [E-MTAB-533] GENCODE Targeted Sequencing Batch III

summary:
As part of the RNASeq Genome Annotation Assessment Project (RGASP) selected novel gene model predictions were analysed with RT-PCR-Seq.

ArrayExpress Release Date: 2011-03-01

Publication Title: GENCODE: producing a reference annotation for ENCODE
Publication Author List: Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R, Swarbreck D, Rossier C, Ucla C, Hubbard T, Antonarakis SE, Guigo R

Person Roles:  submitter
Person Last Name: Kokocinski
Person First Name: Felix
Person Mid Initials:
Person Email: fsk@sanger.ac.uk
Person Phone: -498006
Person Address: Wellcome Trust Genome Campus, Hinxton, UK
Person Affiliation: Wellcome Trust Sanger Institute

Person Roles:  investigator
Person Last Name: Hubbard
Person First Name: Tim
Person Mid Initials:
Person Email: th@sanger.ac.uk
Person Phone: -498055
Person Address: Wellcome Trust Genome Campus, Hinxton, UK
Person Affiliation: Wellcome Trust Sanger Institute

Person Roles:  investigator
Person Last Name: Reymond
Person First Name: Alexandre
Person Mid Initials:
Person Email: Alexandre.Reymond@unil.ch
Person Phone:
Person Address: Lausanne, Switzerland
Person Affiliation: University of Lausanne

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

sample_organism:
Caenorhabditis elegans
Homo sapiens

platform_organism:
Caenorhabditis elegans
Homo sapiens

overall_design:
Experimental Design: co-expression_design
Experimental Design: high_throughput_sequencing_design
Experimental Factor Name: ORGANISM
Experimental Factor Type: organism


title: [E-MTAB-451] Schistosoma mansoni transcriptomics at different life stages

summary:
High-throughput sequencing of life stages and tissues of the flatworm Schistosoma mansoni to be used for further gene editing, gene finding and transcriptome analysis

ArrayExpress Release Date: 2010-12-09

Person Roles: investigator
Person Last Name: Protasio
Person First Name: Anna
Person Mid Initials: V.
Person Email: ap6@sanger.ac.uk
Person Phone:
Person Address: Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, Uk
Person Affiliation: Wellcome Trust Sanger Institute

Person Roles: submitter
Person Last Name: Service
Person First Name: Submission
Person Mid Initials:
Person Email: datahose@sanger.ac.uk
Person Phone:
Person Address: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom
Person Affiliation: Wellcome Trust Sanger Institute

overall_design:
Experimental Design: development_or_differentiation_design
Experimental Design: in_vitro_design
Experimental Design: co-expression_design
Experimental Design: high_throughput_sequencing_design
Experimental Factor Name: DEVELOPMENTALSTAGE
Experimental Factor Type: developmental_stage


title: [E-MTAB-445] Transcription profiling by high throughput sequencing of blackface sheep infected with the gastrointestinal helminth Teladorsagia circumcincta to analyse resistance to infection

summary:
Blackface Teladorsagia Solexa
Analysis of resistance to Teladosagia

ArrayExpress Release Date: 2010-12-08
Publication Author List: Pemberton, J.; Beraldi, D.; Craig, B. and Hopkins, J.

Publication Title: Digital gene expression analysis of gastrointestinal helminth resistance in Scottish blackface lambs
Publication Author List: Sylvain Aubry, Mali Salmon, Kim M Rutherford, Paul Bertone, Andrea Brautigam, Andreas PM Weber, Krystyna A Kelly, Julian M Hibberd

Publication Title: De novo transcriptome assembly enables quantitative expression analysis in non-sequenced model organisms

Person Roles:  submitter
Person Last Name: Hopkins
Person First Name: John
Person Mid Initials:
Person Email: john.hopkins@ed.ac.uk
Person Phone: 44 131 650 6160
Person Address: Roslin Institute, Summerhall, Edinburgh. EH9 1QH. UK
Person Affiliation: University of Edinburgh

overall_design:
Experimental Design: growth_condition_design
Experimental Design: co-expression_design
Experimental Factor Name: CLINICALINFORMATION
Experimental Factor Name: GROWTHCONDITION
Experimental Factor Type: clinical_information
Experimental Factor Type: growth_condition


title: [E-MTAB-434] Transcription profiling by high throughput sequencing of zebra fish tissues and developmental stages

summary:
Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages using the Illumina Genome Analyzer
Paired-end sequence data has been generated using polyA selected RNA from a range of zebrafish tissues and developmental stages using the Illumina Genome Analyzer. These data have been used to improve the gene annotation of the zebrafish genome. Study description: Zebrafish total RNA was extracted from embryonic and adult tissue, then polyA selected. After fragmentation and reverse transcription Illumina sequencing libraries were prepared. Paired-end sequence runs were performed with 36, 37, 54 and 76 base reads on the Illumina Genome Analyzer.

ArrayExpress Release Date: 2011-03-11

Person Roles:  submitter
Person Last Name: Collins
Person First Name: John
Person Mid Initials: E
Person Email: jec@sanger.ac.uk
Person Phone: 01233 834244
Person Address: Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1HH, United Kingdom
Person Affiliation: Wellcome Trust Sanger Institute

overall_design:
Experimental Design: development_or_differentiation_design
Experimental Factor Name: AGE
Experimental Factor Name: DEVELPOMENTAL_STAGE
Experimental Factor Name: ORGANISM_PART
Experimental Factor Type: age
Experimental Factor Type: developmental_stage
Experimental Factor Type: organism_part


title: [E-MTAB-315] RNA-seq of Drosophila S2 cells after RNAi knock-down of signal transduction components

summary:
RNAi of signal transduction components in Drosophila S2 cells
We performed RNAi knockdown experiments on 15 different signal transduction components in Drosophila S2 cells and prepared RNA libraries from the poly-adenylated fraction of the RNA. SOLiD sequencing of strand-specific, barcoded transcriptome libraries yielded expression profiles allowing us to extract  common pathway signatures and indicated that Cka may function as novel regulator in Ras/MAPK signaling.

ArrayExpress Release Date: 2011-07-08

Person Roles:  investigator
Person Last Name: Boutros
Person First Name: Michael
Person Email: m.boutros@dkfz.de
Person Address: Deutsches Krebsforschungszentrum, Signaling and Functional Genomics (B110), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
Person Affiliation: Signaling and Functional Genomics, DKFZ

Person Roles:  investigator
Person Last Name: Sandmann
Person First Name: Thomas
Person Email: t.sandmann@dkfz.de
Person Address: Deutsches Krebsforschungszentrum, Signaling and Functional Genomics (B110), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
Person Affiliation: Signaling and Functional Genomics, DKFZ

Person Roles:  investigator
Person Last Name: Horn
Person First Name: Thomas
Person Email: t.horn@dkfz.de
Person Address: Deutsches Krebsforschungszentrum, Signaling and Functional Genomics (B110), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
Person Affiliation: Signaling and Functional Genomics, DKFZ

Person Roles:  submitter
Person Last Name: Kerr
Person First Name: Grainne
Person Email: g.kerr@dkfz.de
Person Address: Deutsches Krebsforschungszentrum, Signaling and Functional Genomics (B110), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
Person Affiliation: Signaling and Functional Genomics, DKFZ

overall_design:
Experimental Design: cellular_modification_design
Experimental Design: in_vitro_design
Experimental Design: co-expression_design
Experimental Design: transcription profiling by high throughput sequencing
Experimental Factor Name: RNAI
Experimental Factor Type: cellular_modification
Quality Control Type: biological_replicate


title: [E-MTAB-444] Transcription profiling by high throughput sequencing of Cleome gynandra developing and mature leaves

summary:
Cleome gynandra leaf development RNA-seq
RNA-seq have been performed on developing (2mm length) and mature (10mm length) leaves of the C4 photosynthesis plant Cleome gynandra. 6 runs of Illumina 36-42 bp single end have been performed

ArrayExpress Release Date: 2010-12-01
Publication Author List: Sylvain Aubry, Mali Salmon, Kim M Rutherford, Paul Bertone, Andrea Brautigam, Andreas PM Weber, Krystyna A Kelly, Julian M Hibberd

Publication Title: De novo transcriptome assembly enables quantitative expression analysis in non-sequenced model organisms

Person Roles:  submitter
Person Last Name: Aubry
Person First Name: Sylvain
Person Mid Initials:
Person Email: sa530@cam.ac.uk
Person Phone: +441223 330 220
Person Address: Department of Plant Sciences. University of Cambridge. Downing Street. CB2 3EA Cambridge
Person Affiliation: University of Cambridge

overall_design:
Experimental Design: development_or_differentiation_design
Experimental Factor Name: DEVELOPMENTALSTAGE
Experimental Factor Type: developmental_stage
Quality Control Type: biological_replicates


title: Transcriptomic analysis of autistic brain reveals convergent molecular pathology [high-throughput sequence data]

status: Public on Jul 12 2011

first: Xinchen

last: Wang

address: 32 Vassar St, D514

institute: MIT

summary: Autism spectrum disorder (ASD) is a common, highly heritable neurodevelopmental condition characterized by marked genetic heterogeneity. Thus, a fundamental question is whether autism represents an aetiologically heterogeneous disorder in which the myriad genetic or environmental risk factors perturb common underlying molecular pathways in the brain. Here, we demonstrate consistent differences in transcriptome organization between autistic and normal brain by gene co-expression network analysis. Remarkably, regional patterns of gene expression that typically distinguish frontal and temporal cortex are significantly attenuated in the ASD brain, suggesting abnormalities in cortical patterning. We further identify discrete modules of co-expressed genes associated with autism: a neuronal module enriched for known autism susceptibility genes, including the neuronal specific splicing factor A2BP1 (also known as FOX1), and a module enriched for immune genes and glial markers. Using high-throughput RNA sequencing we demonstrate dysregulated splicing of A2BP1-dependent alternative exons in the ASD brain. Moreover, using a published autism genome-wide association study (GWAS) data set, we show that the neuronal module is enriched for genetically associated variants, providing independent support for the causal involvement of these genes in autism. In contrast, the immune-glial module showed no enrichment for autism GWAS signals, indicating a non-genetic aetiology for this process. Collectively, our results provide strong evidence for convergent molecular abnormalities in ASD, and implicate transcriptional and splicing dysregulation as underlying mechanisms of neuronal dysfunction in this disorder.

overall_design: To identify potential A2BP1-dependent differential splicing events in ASD brain, we performed high-throughput RNA sequencing (RNA-Seq) on three autism samples with significant downregulation of A2BP1 (average fold change by quantitative RT-PCR = 5.9) and three control samples with average A2BP1 levels. The list of potential A2BP1-depending differential splicing events in ASD is given in the Supplementary file linked at the foot of this record.

last: Voineagu

first: Patrick

last: Johnston

first: Jennifer

last: Lowe

first: Yuan

last: Tian

first: Steve

last: Horvath

first: Jonathan

last: Mill

first: Rita

last: Cantor

first: Benjamin

last: Blencowe

first: Daniel

middle: H

last: Geschwind


title: [E-MTAB-442] ChIP-seq of mouse liver with no antibody to provide input sequences for ChIP experiments on C57BJ/6J mice

first: ArrayExpress

last: EBI

summary:
Odom_mouse_C57BL6J_input
This experiment provides chromatin immunoprecipitation input sequences (i.e. no antibody was added during the ChIP protocol), suitable for use as input for ChIP experiments on C57BJ/6J mice.

ArrayExpress Release Date: 2011-03-01

Publication Title: Pol III occupancy of tRNA genes is highly divergent between loci but highly conserved by amino acid isotypes
Publication Author List: Claudia Kutter; Gordon D. Brown; Stephen Watt; Michael D. Wilson; Angela Goncalves; Robert J. White, Duncan T. Odom

Person Roles:  submitter
Person Last Name: Brown
Person First Name: Gordon
Person Mid Initials: D
Person Email: gordon.brown@cancer.org.uk
Person Phone: +44(0)1223404275
Person Address: Cancer Research UK, Robinson Way, Cambridge, CB2 0RE, UK
Person Affiliation: CRUK-CRI

overall_design:
Experimental Design: species_design
Experimental Design: replicate_design
Experimental Factor Name: SPECIES
Experimental Factor Name: TISSUE
Experimental Factor Name: ChIP
Experimental Factor Type: organism
Experimental Factor Type: organism_part
Experimental Factor Type: immunoprecipitate
Quality Control Type: biological_replicate


title: Genome wide mapping for TF binding sites for Pol II, JunD, cFos, Max & cMyc in GM12878 (ENCODE Project)

status: Public on Jul 09 2011

city: New Haven

first: Joel

last: Rozowsky

address: 266 Whitney Ave, Bass 437

department: Molecular Biophysics & Biochemistry

institute: Yale University

summary:
We performed ChIP-Seq for 5 different transcription factors (Pol II, JunD, cFos, Max and cMyc) as part of the ENCODE project in order to determine sites of allele-specific binding. This was done in the GM12878 cell line which was genotyped as part of the pilot II phase of the 1000 genomes project. There is a matching RNA-Seq experiemnt performed on the same cell line.

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

overall_design: Mapping TF binding sites for 5 different TFs to assess allele-specific binding

first: Debahish

last: Raha

last: Snyder

first: Mark

last: Gerstein


title: AlleleSeq: Analysis of Allele-Specific Expression and Binding in a Network Framework

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

This SuperSeries is composed of the SubSeries listed below.

relation:
SuperSeries of: GSE30399
SuperSeries of: GSE30400

overall_design: Refer to individual Series


title: RNA-Seq in GM12878 (ENCODE Project)

summary:
We performed RNA-Seq as part of the ENCODE project in order to determine sites of allele-specific expression This was done in the GM12878 cell line which was genotyped as part of the pilot II phase of the 1000 genomes project. There is a matching ChIP-Seq experiments for a number of transcription factors were also performed on the same cell line.

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

overall_design: Transcriptome mapping using RNA-Seq for GM12878


title: Genome-wide maps of epigenetic features in G1E model and in mouse primary erythroblasts.

status: Public on Jul 05 2011

city: University Park

first: Ross

last: Hardison

address: 303 Wartik Lab

institute: Pennsylvania State University

summary: Interplays among lineage specific nuclear proteins, chromatin modifying enzymes and the basal transcription machinery govern cellular differentiation, but their dynamics of actions and coordination with transcriptional control are not fully understood. Alterations in chromatin structure appear to establish a permissive state for gene activation at some loci but they play an integral role in activation at other loci. To determine the predominant roles of chromatin states and factor occupancy in directing gene regulation during differentiation, we mapped chromatin accessibility, histone modifications, and nuclear factor occupancy genome-wide during mouse erythroid differentiation dependent on the master regulatory transcription factor GATA1. Remarkably, despite extensive changes in gene expression, the chromatin state profiles (proportions of a gene in a chromatin state dominated by activating or repressive histone modifications) and accessibility remain largely unchanged during GATA1-induced erythroid differentiation. In contrast, gene induction and repression are strongly associated with changes in patterns of transcription factor occupancy. Our results indicate that during erythroid differentiation, the broad features of chromatin states are established at the stage of lineage commitment, largely independently of GATA1. These determine permissiveness for expression, with subsequent induction or repression mediated by distinctive combinations of transcription factors.

overall_design: Using ChIP-Seq technology to examine DNase hypersensitivity, three transcription factors, and four histone modifications in Gata1-null murine G1E line and rescued G1E-ER4 subline, and also two of the transcription factors in mouse primary erythroblasts. ChIP input DNA was sequenced in each cell type as controls.

first: Weisheng

last: Wu

first: Yong

last: Cheng

first: Cheryl

last: Keller

first: Swathi

last: Kumar

first: Tejaswini

last: Mishra

first: Christapher

last: Morrissey

first: Christine

last: Dorman

first: Deepti

last: Jain

first: Daniela

last: Drautz

first: Yoichiro

last: Shibata

first: Maxim

last: Pimkin

first: Kuan-Bei

last: Chen

first: Jason

last: Ernst

first: Belinda

last: Giardine

first: Lingyun

last: Song

first: Terrence

last: Furey

first: Manolis

last: Kellis

first: Webb

last: Miller

first: James

last: Taylor

first: Stephan

last: Schuster

first: Yu

last: Zhang

first: Francesca

last: Chiaromonte

first: Gerd

last: Blobel

first: Mitchell

last: Weiss

first: Gregory

middle: E

last: Crawford


title: Genome-wide Analysis Reveals Conserved and Divergent Features of Notch1/RBPJ Binding in Human and Murine T Lymphoblastic Leukemia Cells

status: Public on Jul 06 2011

city: Boston

last: Zou

address: 185 Cambridge St.

institute: Harvard University

summary: Notch1 regulates gene expression by associating with the DNA-binding factor RBPJ and is oncogenic in murine and human T cell progenitors. Using ChIP-Seq, we find that in human and murine T-LL genomes Notch1 binds preferentially to promoters, to RBPJ binding sites, and near imputed ZNF143, Ets and Runx sites. ChIP-Seq confirmed that ZNF143 binds to ~40% of Notch1 sites. Notch1/ZNF143 sites are characterized by high Notch1 and ZNF143 signals, frequent co-binding of RBPJ (generally through sites embedded within ZNF143 motifs), strong promoter bias, and relatively low mean levels of activating chromatin marks. RBPJ and ZNF143 binding to DNA is mutually exclusive in vitro, suggesting RBPJ/Notch1 and ZNF143 complexes exchange on these sites in cells. K-means clustering of Notch1 binding sites and associated motifs identified conserved Notch1-Runx, Notch1-Ets, Notch1-RBPJ, Notch1-ZNF143, and Notch1-ZNF143-Ets clusters with different genomic distributions and levels of chromatin marks. Although Notch1 binds mainly to gene promoters, ~75% of direct target genes lack promoter binding and are presumably regulated by enhancers, which were identified near MYC, DTX1, IGF1R, IL7R and the GIMAP cluster. Human and murine T-LL genomes also have many sites that bind only RBPJ. Murine RBPJ âonlyâ sites are highly enriched for imputed REST sites, whereas human RPBJ âonlyâ sites lack REST motifs and are more highly enriched for imputed CREB sites. Thus, there is a conserved network of cis-regulatory factors that interacts with Notch1 to regulate gene expression in T-LL cells, as well as novel classes of divergent RBPJ âonlyâ sites that also likely regulate transcription.

overall_design: Notch1, RBPJ, histone methylation ChIP-seq in human and mouse T-LL cell lines

first: Hongfang

last: Wang

middle: Y

first: Jon

last: Aster


title: Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation

status: Public on Jul 01 2011

city: Huntsville

last: Gertz

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute

summary: To assess variation and inheritance of genome-wide patterns of DNA methylation simultaneously in humans, we applied reduced representation bisulfite sequencing (RRBS) to somatic DNA from six members of a three-generation family.

overall_design: Reduced representation bisulfite sequencing was applied to genomic DNA from leukocytes of 6 family members and two unrelated individuals.

first: Richard

middle: M

last: Myers


title: [E-MTAB-475] Trypanosoma vivax Y486 bloodstream stage RNAseq

first: ArrayExpress

last: EBI

summary:
Trypanosoma vivax is a vector-borne blood parasite of cattle throughout sub-saharan Africa. For some years the genome sequence of this organism has been in development at the Wellcome Trust Sanger Institute and is shortly to be completed. Analysis of the genome has revealed various putative genes encoding unknown proteins. In an effort to validate these features we will sequence mRNA transcripts from the bloodstream stage of the genome strain Y486. Most of the novel gene families identified from the genome sequence are too diverse to be validated individually, i.e. through RT-PCR, so it is necessary to sequence all cellular transcripts. We hope to confirm the transcription of one or all members of the novel gene families from the resulting transcriptome. While essential for the scientific rigour of the present genome project, this transcriptome will also provide an additional resource for the longer-term benefit of the research community.

ArrayExpress Release Date: 2011-02-16

Person Roles:  submitter
Person Last Name: Quan
Person First Name: Lin
Person Mid Initials:
Person Email: ql3@sanger.ac.uk
Person Phone: 01223 834244
Person Address: Wellcome Trust Genome Campus,Hinxton,Cambridge. CB10 1SA UK
Person Affiliation: Wellcome Trust Sanger Institute

Person Roles:  Investigator
Person Last Name: Jackson
Person First Name: Andrew
Person Mid Initials: P
Person Email: aj4@sanger.ac.uk
Person Phone: 01223 834244
Person Address: Wellcome Trust Genome Campus,Hinxton,Cambridge. CB10 1SA UK
Person Affiliation: Wellcome Trust Sanger Institute

Person Roles:  Project Coordinator
Person Last Name: Sanders
Person First Name: Mandy
Person Mid Initials: J
Person Email: mjs@sanger.ac.uk
Person Phone: 01223 834244
Person Address: Wellcome Trust Genome Campus,Hinxton,Cambridge. CB10 1SA UK
Person Affiliation: Wellcome Trust Sanger Institute

overall_design:
Experimental Design: genotype_design
Experimental Design: in_vivo_design
Experimental Design: is_expressed_design
Experimental Design: transcript_identification_design
Experimental Factor Name: StrainOrLine
Experimental Factor Type: StrainOrLine


title: miRNA profiling during adipogenic differentiation of adipose-derived stem cells

status: Public on Jul 04 2011

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary: human Multipotent Adipose-Derived Stem (hMADS) cells were subjected to adipogenic differentiation in vitro and microRNA expression was analyzed during differentiation.

overall_design: Total RNA was extracted at day 0 (AD0), day 3 (AD3) and day 8 (AD8) of differentiation, two biological replicates (1) and (2),  and microRNA profiles were established with SOLiD sequencing.

first: L

last: Zaragosi

first: P

last: Barbry

first: K