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Series GSE48032 Query DataSets for GSE48032
Status Public on May 14, 2014
Title The ABRF Next-Generation Sequencing Study (ABRF-NGS): Multi-platform and cross-methodological reproducibility of transcriptome profiling by RNA-seq [454 GS FLX Titanium]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Next-generation sequencing (NGS) technology applications like RNA-sequencing (RNA-seq) have dramatically expanded the potential for novel genomics discoveries, but the proliferation of various platforms and protocols for RNA-seq has created a need for reference data sets to help gauge the performance characteristics of these disparate methods. Here we describe the results of the ABRF-NGS Study on RNA-seq, which leverages replicate experiments across multiple sites using two reference RNA standards tested with four protocols (polyA selected, ribo-depleted, size selected, and degraded RNA), and examined across five NGS platforms (Illumina’s HiSeqs, Life Technologies’ Personal Genome Machine and Proton, Roche 454 GS FLX, and Pacific Biosciences RS). These results show high (R2 >0.9) intra-platform consistency across test sites, high inter-platform concordance (R2 >0.8) for transcriptome profiling, and a large set of novel splice junctions observed across all platforms. Also, we observe that protocols using ribosomal RNA depletion can both salvage degraded RNA samples and also be readily compared to polyA-enriched fractions. These data provide a broad foundation for standardization, evaluation and improvement of RNA-seq methods.
 
Overall design Two reference RNA standards tested with four protocols (polyA selected, ribo-depleted, size selected, and degraded RNA), and examined across five NGS platforms (Illumina’s HiSeqs, Life Technologies’ Personal Genome Machine and Proton, Roche 454 GS FLX, and Pacific Biosciences RS).

Please note that the samples were named following the ABRF-Platform-Site-Sample-Replicate# format. For example, ABRF-454-CNL-A-1 means Sample A was run on 454 platform at Cornell and this is the first replicate, and ABRF-454-CNL-A-2 means the same exact sample was ran with same machine at same location and is 2nd replicate.
 
Contributor(s) Mason C
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Jun 17, 2013
Last update date May 15, 2019
Contact name Christopher E Mason
Organization name Weill Cornell Medical College
Department Physiology and Biophysics
Lab Christopher Mason Lab
Street address 1305 York Ave
City New York
ZIP/Postal code 10065
Country USA
 
Platforms (1)
GPL14603 454 GS FLX Titanium (Homo sapiens)
Samples (12)
GSM1166026 ABRF-454-CNL-A-1
GSM1166027 ABRF-454-CNL-A-2
GSM1166028 ABRF-454-CNL-B-1
This SubSeries is part of SuperSeries:
GSE46876 The ABRF Next-Generation Sequencing Study (ABRF-NGS): Multi-platform and cross-methodological reproducibility of transcriptome profiling by RNA-seq.
Relations
BioProject PRJNA208734
SRA SRP026123

Download family Format
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE48032_454.counts.txt.gz 340.5 Kb (ftp)(http) TXT
Raw data are available in SRA
Processed data is available on Series record

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