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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 26, 2012 |
| Title |
Targeted RT-PCR assays spanning unannotated splice junctions sequenced by Roche 454. |
| Project |
ENCODE
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| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The ENCODE projects seeks to identify and characterize functional elements in the human genome. Throughout the scale-up phase of ENCODE, the transcriptome group has generate Long RNA-Seq, Small RNA-Seq, Cap-Analysis of Gene Expression (CAGE), and RNA-PET short read data on the Illumina platform for ~ 40 different human primary and transformed cell lines in replicate. From these data several high-resolution and discrete features/elements have been mined out (5’ caps, splice junctions, polyadenylation sites, small RNAs, etc…). However, because these data are obtained from short-read data, we have only limited “connectivity” information. For example, from the long RNA-Seq data, which was sequenced in mate-pair fashion with average insert sizes ~ 200 bp, we know that the sequence from mate 1 is physically linked to the sequence in mate 2. We don’t know the sequence in between and we don’t know how this mate-pair is connected to other mate-pairs in the context of longer transcripts in vivo. To date, this information is gleaned from models generated in silico: In our case, by the program Cufflinks. Consequently, we have a collection of transcript models exhibiting a vast array of local complexity assembled from short read data that need to be experimentally tested. Alternatively, one can “cut to the chase” and use a more raw/elemental form of the data as a basis for additional experimentation to clone out the longer sequences generated in vivo.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
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| Overall design |
454 Data from HepG2, HUVEC, and H1 ES cells
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| Web link |
http://www.ncbi.nlm.nih.gov/geo/info/ENCODE.html
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| Contributor(s) |
Gingeras T, Davis C |
| Citation(s) |
22955620 |
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| Submission date |
Jun 22, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Julien Lagarde |
| E-mail(s) |
julienlag@gmail.com
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| Organization name |
CRG
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| Department |
Bioinformatics and Genomics
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| Lab |
Computational Biology of RNA Processing
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| Street address |
Dr. Aiguader 88
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| City |
Barcelona |
| ZIP/Postal code |
08003 |
| Country |
Spain |
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| Platforms (1) |
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| Samples (3) |
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| Relations |
| SRA |
SRP013872 |
| BioProject |
PRJNA169392 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE38886_RAW.tar |
5.0 Gb |
(http)(custom) |
TAR (of PSL) |
| GSE38886_README.txt |
1.8 Kb |
(ftp)(http) |
TXT |
| GSE38886_suppl_files.tar.gz |
20.1 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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