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| Status |
Public on Jun 09, 2017 |
| Title |
Differentially expressed genes from RNA-Seq and functional enrichment results are affected by the choice of single-end versus paired-end reads and stranded versus non-stranded protocols |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We undertook four mammalian transcriptomics experiments to compare the effect of read mapping, feature counting and differential expression analysis using single-end (SE) and paired-end (PE) protocols. For three of these experiments we also compared a non-stranded (NS) and a strand-specific approach to mapping the paired-end data.
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| Overall design |
Each of the four RNA-Seq experiments had a simple but typical design, comprised of three biological controls and three treated samples. The six samples in each of the experiments were independent biological replicates. Experiments 1 and 2 were from mouse tissue or primary cells whereas Experiments 3 and 4 involved human primary cells and a cell line respectively. In all four experiments sequencing was performed on both ends of the cDNA fragment (paired-end reads). We mapped both ends (see Methods) to produce our paired-end data set (PE data). We also mapped only the first read to produce our single-end read datasets for each experiment (SE data). Sequencing for Experiment 1 occurred in 2012 and used a non-strand-specific protocol for library preparation (Illumina TruSeq kit). The other three experiments were sequenced more recently with the Illumina TruSeq Standed library preparation kit [13]. For these three experiments we looked at the effect of analyzing the paired-end data with a protocol that recognizes the strand-specific nature of the reads (PE data) and also with a protocol that does not recognize this (NS data). In this way we could assess the difference that a strand-specific protocol makes to gene expression analysis.
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| Contributor(s) |
Corley SM, MacKenzie KL, Ali Z, Beverdam A, Mendoza Reinoso V, Roddam LF, Griffin P, Pagnon J, Wilkins MR |
| Citation(s) |
28535780 |
| Submission date |
Apr 06, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Susan Corley |
| E-mail(s) |
s.corley@unsw.edu.au
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| Phone |
+61 02 9385 8853
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| Organization name |
UNSW
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| Department |
Biotechnology & Biomolecular Sciences
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| Lab |
Systems Biology Initiative
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| Street address |
D26, Kensignton Campus
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| City |
Sydney |
| State/province |
NSW |
| ZIP/Postal code |
2052 |
| Country |
Australia |
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| Platforms (3) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (24)
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| Relations |
| BioProject |
PRJNA381932 |
| SRA |
SRP103222 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE97471_Exp1_PE_count_matrix.txt.gz |
297.8 Kb |
(ftp)(http) |
TXT |
| GSE97471_Exp1_SE_count_matrix.txt.gz |
292.1 Kb |
(ftp)(http) |
TXT |
| GSE97471_Exp2_NS_count_matrix.txt.gz |
256.1 Kb |
(ftp)(http) |
TXT |
| GSE97471_Exp2_PE_count_matrix.txt.gz |
241.0 Kb |
(ftp)(http) |
TXT |
| GSE97471_Exp2_SE_count_matrix.txt.gz |
236.5 Kb |
(ftp)(http) |
TXT |
| GSE97471_Exp3_NS_count_matrix.txt.gz |
376.0 Kb |
(ftp)(http) |
TXT |
| GSE97471_Exp3_PE_count_matrix.txt.gz |
335.5 Kb |
(ftp)(http) |
TXT |
| GSE97471_Exp3_SE_count_matrix.txt.gz |
322.4 Kb |
(ftp)(http) |
TXT |
| GSE97471_Exp4_NS_count_matrix.txt.gz |
330.8 Kb |
(ftp)(http) |
TXT |
| GSE97471_Exp4_PE_count_matrix.txt.gz |
312.5 Kb |
(ftp)(http) |
TXT |
| GSE97471_Exp4_SE_count_matrix.txt.gz |
305.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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