|
| Status |
Public on May 11, 2013 |
| Title |
[E-MTAB-1309] GENCODE PCR-Seq Batch IX |
| Project |
ENCODE
|
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
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
|
| |
|
| 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
|
| |
|
| 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 |
| |
|
| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
|
| Samples (8)
|
|
| Relations |
| SRA |
ERP001850 |
| ArrayExpress |
E-MTAB-1309 |
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