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| Status |
Public on Jun 01, 2013 |
| Title |
An integrated 5'- and 3'-end RNA sequencing platform for high-throughput transcriptome quantitation and annotation |
| Organisms |
Drosophila melanogaster; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
RNA-Seq provides an effective way to annotate and measure the transcriptome, but the combination of cost, analysis and end-mapping challenges has limited its adoption for high-throughput quantitation and annotation. Here, we present an integrated experimental and computational suite for transcriptome annotation and quantitation based on the sequencing of mRNA ends. It consists of: a novel, simple, one-step, strategy 5' RNA-Seq; an optimized library construction method for strand-specific 3' RNA-seq that reduces costs and time; and a complete computational analysis toolkit. We demonstrate the power and versatility of our approach to study the transcriptome of LPS stimulation in mouse dendritic cells, promoter structure of the TCRb locus in mouse T cells, and gene expression in circadian cycles in Drosophila. Our platform provides a comprehensive solution for high-throughput, cost-effective transcriptome quantification and end annotation.
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| Overall design |
A study of 5' and 3' end RNA sequencing methods
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| Contributor(s) |
Artyomov M, Kadri S, Bartok O, Shishkin A, Pfiffner J, Ashwal-Fluss R, Amit I, Guttman M, Regev A, Garber M, Kadener S |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
May 23, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Sabah Kadri |
| Organization name |
Broad institute
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| Department |
Computational Biology
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| Street address |
7 Cambridge Center
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| City |
Cambridge |
| State/province |
Massachusetts |
| ZIP/Postal code |
02142 |
| Country |
USA |
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| Platforms (2) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
| GPL13304 |
Illumina HiSeq 2000 (Drosophila melanogaster) |
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| Samples (10)
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| GSM1146899 |
ExoCAGE of BMDCs 0hrs post LPS stimulation |
| GSM1146900 |
ExoCAGE of BMDCs 2hrs post LPS stimulation |
| GSM1146901 |
ExoCAGE of BMDCs 4hrs post LPS stimulation |
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| Relations |
| BioProject |
PRJNA205109 |
| SRA |
SRP023102 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE47207_RAW.tar |
1.0 Mb |
(http)(custom) |
TAR (of BW, TXT) |
| GSE47207_dge3p.genes.table.normalized.txt.gz |
628.5 Kb |
(ftp)(http) |
TXT |
| GSE47207_dge5p.genes.table.normalized.txt.gz |
442.7 Kb |
(ftp)(http) |
TXT |
| GSE47207_dm3.full.scores.rpk.txt.gz |
290.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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