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[E-MTAB-1505] GENCODE PCR-Seq Batch IX

ABSTRACT: Transcription profiling by high throughput sequencing of polyA+ RNAs from eight different human tissues to test a set of de novo transcript models (GENCODE PCR-Seq Batch IX) 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. In batch IX, a set of de novo transcript models was tested aiming to incorporate new long non-coding RNA models into the GENCODE annotation. The original set was built with Cufflinks from ENCODE RNAseq data derived from 15 cell lines by the Gingeras (CSHL) and Wold (CalTech) labs. A subset of multiexonic transcripts not overlapping the GENCODE v10 annotation was selected for this experiment. ArrayExpress Release Date: 2012-10-01 Person Roles: submitter Person Last Name: Gonzalez Person First Name: Jose Person Mid Initials: M Person Email: jmg@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 Person Roles: investigator Person Last Name: Guigo Person First Name: Roderic Person Mid Initials: Person Email: roderic.guigo@crg.cat Person Phone: Person Address: Barcelona, Spain Person Affiliation: Centre for Genomic Regulation (CRG) For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

ORGANISM(S): Homo sapiens

PROVIDER: GSE46639 | GEO | 2013/05/11

REPOSITORIES: GEO

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Project description:Transcription profiling by high throughput sequencing of polyA+ RNAs from eight different human tissues to test a set of de novo transcript models (GENCODE PCR-Seq Batch IX) 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. In batch IX, a set of de novo transcript models was tested aiming to incorporate new long non-coding RNA models into the GENCODE annotation. The original set was built with Cufflinks from ENCODE RNAseq data derived from 15 cell lines by the Gingeras (CSHL) and Wold (CalTech) labs. A subset of multiexonic transcripts not overlapping the GENCODE v10 annotation was selected for this experiment. ArrayExpress Release Date: 2012-10-01 Person Roles: submitter Person Last Name: Gonzalez Person First Name: Jose Person Mid Initials: M Person Email: jmg@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 Person Roles: investigator Person Last Name: Guigo Person First Name: Roderic Person Mid Initials: Person Email: roderic.guigo@crg.cat Person Phone: Person Address: Barcelona, Spain Person Affiliation: Centre for Genomic Regulation (CRG) For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Project description:Transcriptional profiling by high throughput sequencing of RACE-PCR-amplified human brain and testis samples to determine lncRNA transcript 5' and 3'-ends (GENCODE Batch VIII a) As part of the ENCODE consortium the GENCODE project is producing a reference gene set through manual and automated gene prediction. In the current phase of ENCODE we have found strong evidence that many lncRNAs transcript termini are still unknown. This experiment aims to set up an experimental validation strategy to accurately determine the 5' and 3' ends of transcripts, which is based on semi-nested RACE extensions of annotated 5' and 3' ends followed by high throughput sequencing. A total of 400 highly expressed lncRNA transcript models from Gencode 7 which did not have any CAGE/PET support were selected as the test set whereas 25 transcripts with transcript start site (TSS) supported by CAGE tags and transcript termination site (TTS) supported by PET ditags formed the positive control set. Transcript ends were amplified by RACE-PCR from brain and testis RNA samples and sequenced using the Roche 454 platform. The sequencing was performed at the Andalusian Human Genome Sequencing Centre (CASEGH), Seville, Spain. ArrayExpress Release Date: 2012-08-31 Person Roles: submitter Person Last Name: Gonzalez Person First Name: Jose Person Mid Initials: M Person Email: jmg@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 Person Roles: investigator Person Last Name: Guigo Person First Name: Roderic Person Mid Initials: Person Email: roderic.guigo@crg.cat Person Phone: Person Address: Barcelona, Spain Person Affiliation: Centre for Genomic Regulation (CRG) Person Roles: investigator Person Last Name: Santoyo Person First Name: Javier Person Mid Initials: Person Email: jsantoyo@bioinfomgp.org Person Phone: Person Address: Seville, Spain Person Affiliation: Andalusian Human Genome Sequencing Centre (CASEGH) For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

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[E-MTAB-1505] GENCODE PCR-Seq Batch IX

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