Long non-coding RNA expression in Human tissues and cell lines
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE34894 | GEO | 2012/02/01
SECONDARY ACCESSION(S): PRJNA150189
REPOSITORIES: GEO
Similar Datasets
Project description:We designed a custom microarray to profile the expression and used it to measure the expression of 9929 human lncRNAs manually-annotated by the GENCODE group as part of the ENCODE consortium. One microarray hybridisation per biological sample.
2012-02-01 | E-GEOD-34894 | biostudies-arrayexpress
Project description:Our aim was to contribute to a more comprehensive landscape for lncRNA deregulation in NSCLC by identifying lncRNA profiles that could significantly discriminate NSCLCs tissue from paired normal lung tissue. Therefore, we assessed the transcriptional profile of 44 paired tumour and adjacent normal lung tissue from NSCLC patients using an Agilent Custom 8x60K expression array (AMADID: 047718) designed by the GENCODE consortium. This microarray, based on the Gencode v15 catalog of human lncRNA, interrogates 17,535 randomly selected protein coding and 22,001 lncRNA transcripts, being each transcript targeted by two probes.
2019-12-09 | GSE130740 | GEO
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. Batch X targets manually annotated transcripts from GENCODE v11 (released Feb 2012) with novel or putative status, non-pseudogene biotype and unique splice junctions not validated previously.
2012-10-01 | E-MTAB-1310 | biostudies-arrayexpress
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 mouse RNAseq data from the ENCODE project. In Batch M1, which is the first GENCODE validation experiment in mouse, 3148 splice junctions from GENCODE version M2 (released in December 2013) were chosen for experimental verification.
2015-01-22 | E-MTAB-3261 | biostudies-arrayexpress
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 mouse RNAseq data from the ENCODE project. In Batch M2, 808 splice junctions from GENCODE version M4 (released in December 2014) were chosen for experimental verification.
2016-04-28 | E-MTAB-4644 | biostudies-arrayexpress
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
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
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
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 XI 966 splice junctions from GENCODE13 (released July 2012) and 640 splice junctions from GENCODE14 (released October 2012) were chosen for experimental verification.
2013-02-19 | E-MTAB-1505 | biostudies-arrayexpress
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