Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Targeted RT-PCR assays spanning unannotated splice junctions sequenced by Roche 454.

ABSTRACT: The ENCODE projects seeks to identify and characterize functional elements in the human genome. Throughout the scale-up phase of ENCODE, the transcriptome group has generate Long RNA-Seq, Small RNA-Seq, Cap-Analysis of Gene Expression (CAGE), and RNA-PET short read data on the Illumina platform for ~ 40 different human primary and transformed cell lines in replicate. From these data several high-resolution and discrete features/elements have been mined out (5’ caps, splice junctions, polyadenylation sites, small RNAs, etc…). However, because these data are obtained from short-read data, we have only limited “connectivity” information. For example, from the long RNA-Seq data, which was sequenced in mate-pair fashion with average insert sizes ~ 200 bp, we know that the sequence from mate 1 is physically linked to the sequence in mate 2. We don’t know the sequence in between and we don’t know how this mate-pair is connected to other mate-pairs in the context of longer transcripts in vivo. To date, this information is gleaned from models generated in silico: In our case, by the program Cufflinks. Consequently, we have a collection of transcript models exhibiting a vast array of local complexity assembled from short read data that need to be experimentally tested. Alternatively, one can “cut to the chase” and use a more raw/elemental form of the data as a basis for additional experimentation to clone out the longer sequences generated in vivo. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf 454 Data from HepG2, HUVEC, and H1 ES cells

ORGANISM(S): Homo sapiens

SUBMITTER: julien lagarde

PROVIDER: E-GEOD-38886 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Landscape of transcription in human cells.

Djebali Sarah S Davis Carrie A CA Merkel Angelika A Dobin Alex A Lassmann Timo T Mortazavi Ali A Tanzer Andrea A Lagarde Julien J Lin Wei W Schlesinger Felix F Xue Chenghai C Marinov Georgi K GK Khatun Jainab J Williams Brian A BA Zaleski Chris C Rozowsky Joel J Röder Maik M Kokocinski Felix F Abdelhamid Rehab F RF Alioto Tyler T Antoshechkin Igor I Baer Michael T MT Bar Nadav S NS Batut Philippe P Bell Kimberly K Bell Ian I Chakrabortty Sudipto S Chen Xian X Chrast Jacqueline J Curado Joao J Derrien Thomas T Drenkow Jorg J Dumais Erica E Dumais Jacqueline J Duttagupta Radha R Falconnet Emilie E Fastuca Meagan M Fejes-Toth Kata K Ferreira Pedro P Foissac Sylvain S Fullwood Melissa J MJ Gao Hui H Gonzalez David D Gordon Assaf A Gunawardena Harsha H Howald Cedric C Jha Sonali S Johnson Rory R Kapranov Philipp P King Brandon B Kingswood Colin C Luo Oscar J OJ Park Eddie E Persaud Kimberly K Preall Jonathan B JB Ribeca Paolo P Risk Brian B Robyr Daniel D Sammeth Michael M Schaffer Lorian L See Lei-Hoon LH Shahab Atif A Skancke Jorgen J Suzuki Ana Maria AM Takahashi Hazuki H Tilgner Hagen H Trout Diane D Walters Nathalie N Wang Huaien H Wrobel John J Yu Yanbao Y Ruan Xiaoan X Hayashizaki Yoshihide Y Harrow Jennifer J Gerstein Mark M Hubbard Tim T Reymond Alexandre A Antonarakis Stylianos E SE Hannon Gregory G Giddings Morgan C MC Ruan Yijun Y Wold Barbara B Carninci Piero P Guigó Roderic R Gingeras Thomas R TR

Nature 20120901 7414

Eukaryotic cells make many types of primary and processed RNAs that are found either in specific subcellular compartments or throughout the cells. A complete catalogue of these RNAs is not yet available and their characteristic subcellular localizations are also poorly understood. Because RNA represents the direct output of the genetic information encoded by genomes and a significant proportion of a cell's regulatory capabilities are focused on its synthesis, processing, transport, modification ...[more]

PMID: 22955620

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Project description:U87MG is a commonly studied grade IV glioma cell line that has been analyzed in at least 1,700 publications over four decades. In order to comprehensively characterize the genome of this cell line and to serve as a model of broad cancer genome sequencing, we have generated greater than 30x genomic sequence coverage using a novel 50-base mate paired strategy with a 1.4kb mean insert library. A total of 1,014,984,286 mate-end and 120,691,623 single-end two-base encoded reads were generated from five slides. All data were aligned using a custom designed tool called BFAST, allowing optimal color space read alignment and accurate identification of DNA variants. The aligned sequence reads and mate pair information identified 35 interchromosomal translocation events, 1,315 structural variations (>100bp), 191,743 small (<21bp) insertions and deletions (indels), and 2,384,470 single nucleotide variations (SNVs). Among these observations, the known homozygous mutation in PTEN was robustly identified, and genes involved in cell adhesion were overrepresented in the mutated gene list. Data were compared to 219,187 heterozygous single nucleotide polymorphisms assayed by Illumina 1M Duo genotyping array to assess accuracy: 93.83% of all SNPs were reliably detected at filtering thresholds that yield greater than 99.99% sequence accuracy. Protein coding sequences were disrupted predominantly in this cancer cell line due to small indels, large deletions and translocations. In total, 512 genes were homozygously mutated, including 154 by SNVs, 178 by small indels, 145 by large microdeletions and 35 by interchromosomal translocations to reveal a highly mutated cell line genome. Of the small homozygously mutated variants, 8 SNVs and 99 indels were novel events not present in dbSNP. These data demonstrate that routine generation of broad cancer genome sequence is possible outside of genome centers. The sequence analysis of U87MG provides an unparalleled level of mutational resolution compared to any cell line to date. Whole genome sequencing of the U87MG brain cancer cell line using the AB SOLiD3 sequencer and genotyping using the Illumina Human1M-Duov3 DNA Analysis BeadChip

Project description:This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Carrie Davis mailto:davisc@cshl.edu (experimental), Roderic Guigo mailto:rguigo@imim.es and lab (data processing) and Tom Gingeras mailto:gingeras@cshl.edu (primary investigator)). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu). These tracks were generated by the ENCODE Consortia. They contain information about mouse RNAs > 200 nucleotides in length obtained as short reads off the Illumina platform. Data are available from biological replicates. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Tissue Samples: Individual tissues were harvested from mouse strain C57BL/6NJ at different timepoints according to ENCODE cell culture protocols. Whenever possible biological replicates from litermates. Library Preparation: The published cDNA sequencing protocol was used. This protocol generates directional libraries and reports the transcripts' strand of origin. Exogenous RNA spike-ins were added to each endogenous RNA isolate and carried through library construction and sequencing. The spike-in sequence and the concentrations are available for download in the supplemental directory. Sequencing and Mapping: The libraries were sequenced on the Illumina platform (either GAIIx or Hi-Seq) in mate-pair fashion (either pair-end 76 or pair-end 101) to an average depth of 100 million mate-pairs. The data were mapped against hg19 using Spliced Transcript Alignment and Reconstruction (STAR) written by Alex Dobin (CSHL). More information about STAR, including the parameters used for these data, is available from the Gingeras lab. Verification: FPKM (fragments per kilobase of exon per million fragments mapped) values were calculated for annotated exons and Spearman correlation coefficients were computed. In general, Rho values are > .90 between biological replicates.

Dataset Information

Targeted RT-PCR assays spanning unannotated splice junctions sequenced by Roche 454.

Publications

Landscape of transcription in human cells.

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