E-MTAB-1665 - RNA-seq of non coding RNA from five human tissues to determine lncRNA transcript 5' and 3'-ends (GENCODE PCR-Seq Batch VIII c)

Released on 17 May 2013, last updated on 3 May 2014
Homo sapiens
Samples (5)
Protocols (4)
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 RNA samples from five different tissues (heart, kidney, liver, lung and spleen) and sequenced using the Roche 454 platform. The sequencing was performed at the Andalusian Human Genome Sequencing Centre (CASEGH), Seville, Spain.
Experiment types
RNA-seq of non coding RNA, co-expression, organism part comparison, reference
GENCODE: The reference human genome annotation for The ENCODE project. Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken B, Barrell D, Zadissa A, Searle S, Barnes I, Bignell A, Boychenko V, Hunt T, Kay M, Mukherjee G, Rajan J, Despacio-Reyes G, Saunders G, Steward C, Harte R, Lin M, Howald C, Tanzer A, Derrien T, Chrast J, Walters N , Balasubramanian S, Pei B, Tress M, Rodriguez JM, Ezkurdia I, van Baren J , Brent M, Haussler D, Kellis M, Valencia A, Reymond A, Gerstein M, Guigo R, Hubbard T.
Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome. Howald C, Tanzer A, Chrast J, Kokocinski F, Derrien T, Walters N, Gonzalez JM, Frankish A, Aken BL, Hourlier T, Vogel JH, White S, Searle SMJ, Harrow J, Hubbard T, Guigo R, Reymond A.
Exp. designProtocolsVariablesProcessedSeq. reads
Investigation descriptionE-MTAB-1665.idf.txt
Sample and data relationshipE-MTAB-1665.sdrf.txt