E-MTAB-1309 - 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)

Released on 1 October 2012, last updated on 6 November 2012
Homo sapiens
Samples (8)
Protocols (5)
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.
Experiment types
RNA-seq of coding RNA, co-expression, organism part comparison, reference
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.
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.
Exp. designProtocolsVariablesProcessedSeq. reads
Investigation descriptionE-MTAB-1309.idf.txt
Sample and data relationshipE-MTAB-1309.sdrf.txt