Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

GENCODE Targeted Sequencing Batch III

ABSTRACT: As part of the RNASeq Genome Annotation Assessment Project (RGASP) selected novel gene model predictions were analysed with RT-PCR-Seq.

ORGANISM(S): Caenorhabditis elegans

SUBMITTER: Felix Kokocinski

PROVIDER: E-MTAB-533 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

GENCODE: producing a reference annotation for ENCODE.

Harrow Jennifer J Denoeud France F Frankish Adam A Reymond Alexandre A Chen Chao-Kung CK Chrast Jacqueline J Lagarde Julien J Gilbert James G R JG Storey Roy R Swarbreck David D Rossier Colette C Ucla Catherine C Hubbard Tim T Antonarakis Stylianos E SE Guigo Roderic R

Genome biology 20060807

<h4>Background</h4>The GENCODE consortium was formed to identify and map all protein-coding genes within the ENCODE regions. This was achieved by a combination of initial manual annotation by the HAVANA team, experimental validation by the GENCODE consortium and a refinement of the annotation based on these experimental results.<h4>Results</h4>The GENCODE gene features are divided into eight different categories of which only the first two (known and novel coding sequence) are confidently predic ...[more]

PMID: 16925838

Similar Datasets

GENCODE PCR-Seq Batch II

2010-11-01 | E-MTAB-407 | biostudies-arrayexpress

GENCODE PCR-Seq Batch I

2011-05-01 | E-MTAB-612 | biostudies-arrayexpress

GENCODE PCR-Seq Batch IV

Project description: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. This is batch IV, based on chromosome 3, 4 and 5 annotations from Gencode 4 (January 2010). The sequences in this submission were obtained from two different RNA amplifications of the same original RNA for each tissue (called cdna1 and cdna2 in the assay names). In addition testis cDNA1 and lung cDNA2 were sequenced twice (rep1, rep2), and sequences originated from a new dilution of brain and testis cDNA1 (newdil) have also been included.

2011-08-22 | E-MTAB-684 | biostudies-arrayexpress

GENCODE PCR-Seq Batch V

2011-08-22 | E-MTAB-737 | biostudies-arrayexpress

GENCODE PCR-Seq Batch VI

2011-11-25 | E-MTAB-831 | biostudies-arrayexpress

GENCODE PCR-Seq Batch VII

2012-02-01 | E-MTAB-935 | biostudies-arrayexpress

GENCODE PCR-Seq Batch XII

Project description: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 of at least one of their unique splice junctions followed by sequencing. The experiment targets are manually annotated transcripts with novel or putative status, non-pseudogene biotype and unique splice junctions not validated previously. For Batch XII 416 splice junctions from GENCODE15 (released January 2013) were chosen for experimental verification.

2014-11-26 | E-MTAB-3122 | biostudies-arrayexpress

GENCODE PCR-Seq Batch XIV

Project description: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 of at least one of their unique splice junctions followed by sequencing. The experiment targets are manually annotated transcripts with novel or putative status, non-pseudogene biotype and unique splice junctions not validated previously. For Batch XIV 271 splice junctions from GENCODE16 (released April 2013) were chosen for experimental verification.

2014-12-16 | E-MTAB-3168 | biostudies-arrayexpress

GENCODE PCR-Seq Batch XV

Project description: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 of at least one of their unique splice junctions followed by high-throughput sequencing. The experiment targets are manually annotated transcripts with novel or putative status, non-pseudogene biotype and unique splice junctions which have not been validated previously and are not supported by RNAseq data from the ENCODE and GTEx projects. For Batch XV 1243 splice junctions from GENCODE19 (released in December 2013) were chosen for experimental verification.

2014-12-16 | E-MTAB-3169 | biostudies-arrayexpress

GENCODE PCR-Seq Batch XVII

Project description: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 of at least one of their unique splice junctions, followed by high-throughput sequencing (RT-PCR-seq). The experimental targets are manually annotated transcripts with novel or putative status, non-pseudogene biotype, and unique splice junctions which have not been validated previously and are not supported by RNAseq data from the ENCODE and GTEx projects. For Batch XVII, 1159 splice junctions which failed this experimental verification in previous experiments were tested again. On this occasion, newly designed PCR primers were used and compared with the original ones. In addition, the original tissue panel was widened with the inclusion of eight new tissues.

2017-03-31 | E-MTAB-5527 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data