Emanuelsson et al. - High-Density Tiling Microarray Strategies

Full title: Assessing the Performance of Different High-density Tiling Microarray Strategies for Mapping Transcribed Regions of the Human Genome.
Authors: Olof Emanuelsson, Ugrappa Nagalakshmi, Deyou Zheng, Joel S. Rozowsky, Alexander E. Urban, Jiang Du, Zheng Lian, Viktor Stolc, Sherman Weissman, Michael Snyder, Mark Gerstein
Citation info: Genome Research, accepted for publication


Submitted manuscript
Click here to find submitted manuscript (text and figures)

Supplementary Text
.doc format
.pdf format

Supplementary Figures
.ppt format
.pdf format




Note: All genomic coordinates refer to NCBI v 34 (July 2003) unless otherwise stated.

All TAR sets
Placenta MAS-B
Placenta MAS-N
Placenta Affy
NB4 MAS-N
NB4 Affy

All TAR sets, including overlap with (i) the other TAR sets, (ii) Gencode annotation, (iii) a set of conserved regions
Placenta MAS-B w. overlap with other TAR sets: Placenta MAS-N, Placenta Affy, NB4 MAS-N, NB4 Affy; and with Gencode and conserved regions
Placenta MAS-N w. overlap with other TAR sets: Placenta MAS-B, Placenta Affy, NB4 MAS-N, NB4 Affy; and with Gencode and conserved regions
Placenta Affy w. overlap with other TAR sets: Placenta MAS-B, Placenta MAS-N, NB4 MAS-N, NB4 Affy; and with Gencode and conserved regions
NB4 MAS-N w. overlap with other TAR sets: Placenta MAS-B, Placenta MAS-N, Placenta Affy, NB4 Affy; and with Gencode and conserved regions
NB4 Affy w. overlap with other TAR sets: Placenta MAS-B, Placenta MAS-N, Placenta Affy, NB4 MAS-N; and with Gencode and conserved regions
Note: For each TAR, its overlap with the other four TAR sets and with the Gencode annotation and the set of conserved regions is presented in two columns per overlap category: overlap measured (i) in fraction of the length of the TAR, and (ii) in nucleotides.


Transcription status (for all 5 sets)
Exons [median intensity; -log10(pvalue); #probes above median]
Transcripts (splice variants) [median intensity; -log10(pvalue); #probes above median]
For each transcript: Exons called ON=1 or OFF=0

Transcription status of genes (for placenta, MAS-B and Affy)
Genes "on" in MAS and Affy
Genes "on" in MAS only
Genes "on" in Affy only
Genes "off" in both MAS and Affy

Links to raw data in GEO
MAS array platform (GPL2105)
MAS placenta and NB4 data (GSE2720)
Affy array platform (GPL1789)
Affy placenta data (GSE2671)
Affy NB4 data (GSE2679)


PCR validation
PCR primers and corresponding gel lanes (tab-delimited .txt)
Gel pictures (.pdf)


Olof Emanuelsson
Last modified: Mon Jun 12 14:56:40 CEST 2006