RNA-Seq is a method for mapping and quantifying the transcriptome of any
organism that has a genomic DNA sequence assembly. RNA-Seq was performed
by reverse-transcribing an RNA sample into cDNA, followed by high
throughput DNA sequencing on an Illumina Genome Analyser.
This track shows the RNA-seq data published by
Chris Burge's lab
(Wang et al.,2008) mapped to the genome using GEM Mapper
Guigó lab at the Center for Genomic Regulation
(CRG). The subtracks display
RNA-seq data from various tissues/cell lines:
- Lymph Node
- BT474 - Breast Tumour Cell Line
- HME - Human Mammary Epithelial Cell Line
- MCF7 - Breast Adenocarcinoma Cell Line
- MB-435 - Breast Ductal Adenocarcinoma Cell Line*
- T-47D - Breast Ductal Carcinoma Cell Line
Tissues were obtained from unrelated anonymous donors. HME is a mammary
epithelial cell line immortalized with telomerase reverse transcriptase (TERT). The other cell lines are breast cancer cell lines produced from invasive
ductal carcinomas (ATCC).
*NOTE: studies have shown that the MDA-MB-435 cell line appears to have been
contaminated with the M14 melanoma cell line. See this
the American Type Culture Collection (ATCC) website for more details.
Display Conventions and Configuration
This track is a multi-view composite track that contains multiple data types
(views). For each view, there are multiple subtracks that
display individually on the browser. Instructions for configuring multi-view
tracks are here.
The following views are in this track:
- Raw Signal
- Density graph (bedGraph) of signal enrichment based on a normalized aligned
read density (counts per million mapped reads for each subtrack). This
normalized measure assists in visualizing the relative amount of a given
transcript across multiple samples.
- The Alignments view shows reads mapped to the genome.
The group at CRG obtained RNA-seq reads, generated by Wang et al.
(2008), from the Short Read Archive section of GEO at NCBI under accession
number GSE12946. Using their GEM mapper program, CRG mapped the
RNA-seq reads to the genome and transcriptome (GENCODE Release 3, October
2009 Freeze). GEM mapper was run using default parameters and allowing up
to two mismatches in the read alignments. Since mapping to the transcriptome
depends on length of the reads mapped, reads were only mapped for the
14 tissues or cell lines where reads were of length 32 bp. This excluded
reads from MAQC human cell lines (mixed human brain) and MAQC UHR (mixed
human cell lines).
These data were generated by Chris Burge's lab at the Massachusetts Institute
of Technology and by Roderic Guigó's lab at the Center for Genomic
Regulation (CRG) in Barcelona, Spain. GTF files of the mapped data were
provided by Thomas Derrien and Paolo Ribeca from CRG. GEM mapper software
can be obtained
Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB.
Alternative isoform regulation in human tissue transcriptomes.
Nature. 2008 Nov 27;456(7221):470-6.
PMID: 18978772; PMC: PMC2593745