This SuperSeries is composed of the SubSeries listed below.
Overall design: Refer to individual Series
| Accession | PRJNA208232; GEO: GSE47792 |
| Type | Umbrella project |
| Publications (total 6) Less... | - Li D et al., "Impact of Sequencing Depth and Library Preparation on Toxicological Interpretation of RNA-Seq Data in a "Three-Sample" Scenario.", Chem Res Toxicol, 2021 Feb 15;34(2):529-540
More...- Li D et al., "Impact of Sequencing Depth and Library Preparation on Toxicological Interpretation of RNA-Seq Data in a "Three-Sample" Scenario.", Chem Res Toxicol, 2021 Feb 15;34(2):529-540
- Munro SA et al., "Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures.", Nat Commun, 2014 Sep 25;5:5125
- Li S et al., "Detecting and correcting systematic variation in large-scale RNA sequencing data.", Nat Biotechnol, 2014 Sep;32(9):888-95
- SEQC/MAQC-III Consortium "A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium.", Nat Biotechnol, 2014 Sep;32(9):903-14
- Wang C et al., "The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance.", Nat Biotechnol, 2014 Sep;32(9):926-32
- Su Z et al., "An investigation of biomarkers derived from legacy microarray data for their utility in the RNA-seq era.", Genome Biol, 2014 Dec 3;15(12):523
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| Submission | Registration date: 10-Jun-2013
Center for Pharmacogenomics, School of Life Sciences, Fudan Univresity |
| Relevance | Superseries |
Project Data:
| Resource Name | Number
of Links |
|---|
| Sequence data |
| SRA Experiments | 3344 |
| Publications |
| PubMed | 11 |
| PMC | 10 |
| Other datasets |
| BioSample | 4340 |
| GEO DataSets | 11 |
GEO Data Details| Parameter | Value |
|---|
| Data volume, Spots | 25627071 |
| Data volume, Processed Mbytes | 296 |
| Data volume, Supplementary Mbytes | 4001 |
| Parameter | Value |
|---|
| Data volume, Gbases | 5,158 |
| Data volume, Tbytes | 3.49 |
SEQC Project encompasses the following 10 sub-projects:
| Project Type | Number of Projects |
| Transcriptome or Gene expression | 10 |
BioProject
accession | Name | Title |
|---|
| PRJNA208369 | A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequence Quality Control consortium | A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequence Quality Control consortium (Center for Pharmacogenomics,...) | | PRJNA208822 | Homo sapiens | MAQC-III/SEQC Main Study ABCD titration experiment, ERCC spike-in profiles and gene-level estimates for a selected test set (Chair of Bioinformatics,...) | | PRJNA214798 | Homo sapiens | RNA-Seq reveals an unprecedented complexity of the neuroblastoma transcriptome and is suitable for clinical endpoint prediction [microarray] (Systems Toxicology, NCTR/FDA) | | PRJNA214797 | Homo sapiens | RNA-Seq reveals an unprecedented complexity of the neuroblastoma transcriptome and is suitable for clinical endpoint prediction [RNA-Seq] (Center for Pharmacogenomics,...) | | PRJNA243413 | Homo sapiens | A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequence Quality Control consortium (Center for Pharmacogenomics,...) |
List all 10 'Transcriptome or Gene expression' projects...BioProject
accession | Name | Title |
|---|
| PRJNA208369 | A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequence Quality Control consortium | A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequence Quality Control consortium (Center for Pharmacogenomics,...) | | PRJNA208822 | Homo sapiens | MAQC-III/SEQC Main Study ABCD titration experiment, ERCC spike-in profiles and gene-level estimates for a selected test set (Chair of Bioinformatics,...) | | PRJNA214798 | Homo sapiens | RNA-Seq reveals an unprecedented complexity of the neuroblastoma transcriptome and is suitable for clinical endpoint prediction [microarray] (Systems Toxicology, NCTR/FDA) | | PRJNA214797 | Homo sapiens | RNA-Seq reveals an unprecedented complexity of the neuroblastoma transcriptome and is suitable for clinical endpoint prediction [RNA-Seq] (Center for Pharmacogenomics,...) | | PRJNA243413 | Homo sapiens | A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequence Quality Control consortium (Center for Pharmacogenomics,...) | | PRJNA214799 | Homo sapiens | Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data (Medicine, Weill Cornell Medical...) | | PRJNA264621 | Homo sapiens | An Investigation of Biomarkers Derived from Legacy Microarray Data for Their Utility in the RNA-Seq Era (Center for Pharmacogenomics,...) | | PRJNA208229 | Rattus norvegicus | SEQC Toxicogenomics Study: microarray data set (Center for Pharmacogenomics,...) | | PRJNA239561 | Rattus norvegicus | SEQC Toxicogenomics Study: RNA-Seq data set (Center for Pharmacogenomics,...) | | PRJNA238328 | Rattus norvegicus | A rat RNA-Seq transcriptomic Bodymap across eleven organs and four developmental stages (Center for Pharmacogenomics,...) |
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