RNA-Seq CAGE (Cap Analysis of Gene Expression) analysis of human tissues in RIKEN FANTOM5 project
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ABSTRACT:
INSTRUMENT(S): Helicos HeliScope
ORGANISM(S): Homo sapiens
SUBMITTER:
PROVIDER: E-MTAB-3358 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:This experiment captures the expression data reported by the RIKEN FANTOM5 project ( http://fantom.gsc.riken.jp/5/ ), focusing on mice cell data which was deposited in the seqence read archive (SRA) under study accession DRP001032 (https://www.ebi.ac.uk/ena/data/view/DRP001031 ) . The samples in this experiment can also be found on a dedicated page of the FANTOM website: http://fantom.gsc.riken.jp/5/sstar/Browse_samples. Since this is CAGE analsyis, gene expression data is reported by FANTOM5 in TPMs (tags per milliion) for gene promoters. This is in conjunction with E-MTAB-3577 (http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3577/)
2015-05-14 | E-MTAB-3578 | biostudies-arrayexpress
Project description:This experiment captures the expression data reported by the RIKEN FANTOM5 project ( http://fantom.gsc.riken.jp/5/ ), focusing on mice tissue data which was deposited in the sequence read archive (SRA) under study accession DRP001032 (https://www.ebi.ac.uk/ena/data/view/DRP001031 ) . The samples in this experiment can also be found on a dedicated page of the FANTOM website: http://fantom.gsc.riken.jp/5/sstar/Browse_samples. Since this is CAGE analysis, gene expression data is reported by FANTOM5 in TPMs (tags per milliion) for gene promoters. This is in conjunction with E-MTAB-3578 (http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3578/)
2015-05-14 | E-MTAB-3579 | biostudies-arrayexpress
Project description:The aim of this experiment was to compare the transciptome of the fall armyworm (Spodoptera frugiperda) strain SUS (a laboratory insecticide-susceptible standard) with organophosphate (OP) and pyrethroid (PYR) resistant strains were collected in cornfields located in Minas Gerais and Mato Grosso States, Brazil, in 2008 and maintained in the laboratory under selection with chlorpyrifos (at increasing discriminating doses from 100 up to 400 M-BM-5g of insecticide/g of insect in a topical bioassay) or lambda-cyhalothrin (from 8.4 up to 27 M-BM-5g of insecticide/g of insect) respectively The custom microarray used in this study was designed using the Agilent eArray platform (Agilent Technologies). A SurePrint HD (8M-CM-^W15k) expression array was designed using the base composition and the best probe methodologies to design sense orientation 60-mer probes with a 3M-bM-^@M-2 bias. The FAW EST database (SPODOBASE) was used as the reference transcriptome (Negre, Hotelier et al. 2006). These sequences are derived from 8 cDNA libraries as follows: Sf1F: Fat body, Sf1H: Hemocyte, Sf1M: Midgut, Sf1P: Pool of various tissues, Sf2H: Immune Challenged hemocytes, Sf2L: Sf21 Cell lines sequences, Sf2M: Xenobiotic Induced Midgut and Sf9L: Sf9 cell lines sequences. All assembled contigs and singlets were kindly sent by the website maintainers. The BLAST2GO software v.2.3.1 (http://www.blast2go.org) was used to annotate the EST database. 60-mer probes were designed for all 7,552 assembled contigs and 5,519 annotated singlets (BlastX), totaling 13,071 sequences. For contigs encoding detoxification enzymes (P450s, GSTs and CEs) three probes were designed. Additional probe groups for 15 control genes were also included. For reference all sequences are included in the zip file with array data. References: Negre, V., T. Hotelier, et al. (2006). "SPODOBASE : an EST database for the lepidopteran crop pest Spodoptera." BMC Bioinformatics 7: 322. Two-condition experiment. Slide 1: SUS vs. OP S. fugiperda strains. Slide 2: SUS vs. PYR S. fugiperda strains. Biological replicates: 4 pools of RNA extracted from four pools of 5 second instar larvae. Technical Replicates: None, the biological replicates incorporated a dye swap. Total replication: four replicates for each strain.
2013-08-01 | E-GEOD-43295 | biostudies-arrayexpress
Project description:Transcriptional enhancers play critical roles in regulation of gene expression, but their identification has remained a challenge. Recently, it was shown that enhancers in the mammalian genome are associated with characteristic histone modification patterns, which have been increasingly exploited for enhancer identification. However, only a limited number of histone modifications have previously been investigated for this purpose, leaving the questions answered whether there exist an optimal set of histone modifications that could improve the enhancer prediction. Here, we address this issue by exploring a rich dataset produced by the human Epigenome Roadmap Project. Specifically, we examined genome-wide profiles of 24 histone modifications in human embryonic stem cells and fibroblasts, and developed a Random-Forest based algorithm to integrate histone modification profiles for identification of enhancers.As a training set, we used histone modification profiles at genome-wide binding sites of p300 in the two cell types identified using ChIP-seq. We show that this algorithm not only leads to more accurate and precise prediction of enhancers than previous methods, but also helps identify an optimal set of three chromatin marks for enhancer prediction. ChIP-Seq Analysis of p300 in hESC H1 and IMR90 cells. Sequencing was done on the Illumina Genome Analyzer II platform for the H1 data and Illumina HiSeq for IMR90.Data was mapped to hg18 using Bowtie.
2012-05-09 | E-GEOD-37858 | biostudies-arrayexpress
Project description:A "Cartes d'Identite des Tumeurs" (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net). We compared the relative precision and accuracy of expression measurements obtained from three different state-of-the-art commercial short and long-oligonucleotide microarray platforms (Affymetrix GeneChipTM, GE Healthcare CodeLinkTM and Agilent Technologies). The design of the comparison was chosen to judge each platform in the context of a multi-project program. The analyses were based on data from three biologically distinct human cell lines and a non-redundant set of roughly 3,400 targets chosen for their unique correspondence toward a single transcript. Raw data from the following were studied : 12 Affymetrix HG-U133 plus 2.0 GeneChipTM arrays (3 arrays per sample type independently labeled, March, 2004); 12 Agilent's "44K whole genome" arrays (4 arrays per cell line; 3 arrays for 3 independent labeling reactions plus one technical replicate, June 2004); 12 Amersham CodeLinkTM UniSet Human 20K Human arrays (3 slides per sample type labeled in batch, March, 2004).
2005-11-01 | E-MEXP-467 | biostudies-arrayexpress
Project description:The use of induced pluripotent stem cells (iPSC) derived from independent patients and sources holds considerable promise to improve the understanding of development and disease. However, optimized use of iPSC depends on our ability to develop methods to efficiently qualify cell lines and protocols, monitor genetic stability, and evaluate self-renewal and differentiation potential. To accomplish these goals, 57 stem cell lines from 10 laboratories were differentiated to 7 different states, resulting in 248 analyzed samples. Cell lines were differentiated and characterized at a central laboratory using standardized cell culture methodologies, protocols, and metadata descriptors. Stem cell and derived differentiated lines were characterized using RNA-seq, miRNA-seq, copy number arrays, DNA methylation arrays, flow cytometry, and molecular histology. All materials, including raw data, metadata, analysis and processing code, and methodological and provenance documentation are publicly available for re-use and interactive exploration at https://www.synapse.org/pcbc . The goal is to provide data that can improve our ability to robustly and reproducibly use human pluripotent stem cells to understand development and disease. 114 samples This submission represents DNA methylation component of study.
2016-08-20 | E-GEOD-85828 | biostudies-arrayexpress
Project description:Compilation fo whole genome gene expression changes in Staphylococcus aureus USA300 LAC cultures grown in the presence of vehicle or the anti-gout drug benzbromarone. The drug was intially screened as effective against the agr quorum sensing system in Staphylococcus aureus AH1677. A microarray study using total RNA harvested from three cultures of Staphylococcus aureus USA300 LAC plus vehicle control and three cultures of Staphylococcus aureus USA300 LAC plus 12 uM benzbromarone.
2014-03-19 | E-GEOD-55980 | biostudies-arrayexpress
Project description:Human embryonic stem cells share identical genomic sequences with other lineage-committed cells yet possess the remarkable properties of self-renewal and pluripotency. It has been proposed that epigenetic regulatory mechanisms, involving DNA methylation and various chromatin modifications, are at least partly responsible for the distinct cellular properties between different cell types. Previous studies focusing largely on gene promoters and CpG islands have identified close association between several chromatin modifications and DNA methylation, but revealed a relatively small degree of differences between pluripotent and lineage-committed cells. Here, we examine the association between 11 chromatin modifications and DNA methylation at high resolution throughout the genome in the human embryonic stem cells and primary fetal lung fibroblasts. We observe a new set of relationships between chromatin modifications and DNA methylation occurring outside of the promoter regions. We also find that epigenomic landscapes are drastically different between the ES cells and fibroblasts. In particular, over 40% of the human genome differs in their chromatin structure between the two cell types. Most of the changes come from a dramatic redistribution of the repressive H3K9me3 and H3K27me3 marks, which form large blocks that expand significantly in the fibroblasts relative to ES cells. Additionally, we identified numerous small and punctuated regions outside of promoters that are associated with many active chromatin modification marks, and show that chromatin dynamics at these potential regulatory sequences are associated with change in DNA methylation between the ES cells and fibroblasts. Our results provide new insights into epigenetic regulatory mechanisms underlying properties of pluripotency and cell fate commitment. ChIP-Seq Analysis of OCT4, KLF4, MYC, TAFII and P300 in hESC H1 cells. 36 cycles of sequencing was done on the Illumina Genome Analyzer or Analyzer II platforms.
2009-10-13 | E-GEOD-17917 | biostudies-arrayexpress
Project description:Human embryonic stem cells (hESCs) are offering a new therapeutic approach because of their unique ability to proliferate indefinitely in vitro and differentiate into multiple cell types. However, our understanding of the molecular mechanisms of pluripotency and self-renewal remain incomplete. To elucidate the key regulatory sequences and genes responsible for these cellular properties, we have determined potential enhancers and insulators in the genome of human ES cells and examined the dynamics of four key chromatin modifications (H3K4me1, H3K4me3, H3K27ac and H3K27me3) at both promoters and enhancers during the differentiation of these cells. We observe that most enhancers gain or lose H3K4me1 and H3K27ac during differentiation in a manner that correlates with expression of their potential target genes. By contrast, chromatin modifications at promoters remain stable and largely invariant during hESC differentiation, with the exception of a small number of promoters where a dynamic switch between acetylation and methylation at H3K27 marks the transition between activation and silencing of gene expression. Our results reveal more than 50,000 potential enhancers for early human development, and identify key genes that are involved in differentiation and maintenance of pluripotency in human ES cells. ChIP-Seq Analysis of SOX2 and NANOG in hESC H1 cells. 36 cycles of sequencing was done on the Illumina Genome Analyzer II platform.
2009-10-14 | E-GEOD-18292 | biostudies-arrayexpress