|
| Status |
Public on May 11, 2013 |
| Title |
[E-MTAB-1222] GENCODE Batch VIII a: determining lncRNA transcript 5' and 3'-ends by RACE-PCR / 454 sequencing |
| Project |
ENCODE
|
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
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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| |
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| Overall design |
Experimental Design: organism_part_comparison_design
Experimental Design: reference_design
Experimental Design: co-expression_design
Experimental Factor Name: organism part
Experimental Factor Type: organism part
|
| Web link |
http://www.ncbi.nlm.nih.gov/geo/info/ENCODE.html
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| |
|
| Citation(s) |
22955982, 22955987 |
| BioProject |
PRJNA30709 |
| |
| Submission date |
May 03, 2013 |
| Last update date |
May 15, 2019 |
| Organization |
European Bioinformatics Institute |
| E-mail(s) |
miamexpress@ebi.ac.uk
|
| Lab |
ArrayExpress
|
| Street address |
Wellcome Trust Genome Campus
|
| City |
Hinxton |
| State/province |
Cambridgeshire |
| ZIP/Postal code |
CB10 1SD |
| Country |
United Kingdom |
| |
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| Platforms (1) |
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| Samples (2) |
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| Relations |
| SRA |
ERP001793 |
| ArrayExpress |
E-MTAB-1222 |
