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Series GSE94800 Query DataSets for GSE94800
Status Public on Mar 01, 2017
Title Quantification of differential gene expression by multiplexed targeted resequencing of cDNA
Organisms Homo sapiens; synthetic construct
Experiment type Expression profiling by high throughput sequencing
Summary We present an approach for quantification of differential mRNA expression by targeted resequencing of cDNA using single-molecule molecular inversion probes (cDNA-smMIPs), which enable highly multiplexed resequencing of cDNA target regions of ~100 nt and counting of individual molecules. We show that accurate estimates of differential expression can be obtained from molecule counts for hundreds of smMIPs per reaction and that smMIPs are also suitable for quantification of relative gene expression and allele-specific expression. cDNA-smMIPs are a cost-effective tool for hypothesis-driven expression analysis in large numbers of genes (10 to 500) and samples (hundreds to thousands).
Overall design Analysis of differential gene expression using artificial ERCC transcripts and endogeneous transcripts from primary cells and cell lines
Contributor(s) Albers K, Hoischen A
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Submission date Feb 10, 2017
Last update date May 15, 2019
Contact name Kees Albers
Organization name Radboud University Medical Center
Department Human Genetics
Street address Geert Grooteplein 10
City Nijmegen
ZIP/Postal code 6525GA
Country Netherlands
Platforms (2)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL23058 Illumina NextSeq 500 (Homo sapiens; synthetic construct)
Samples (92)
GSM2483289 Sample ERCC1 capture replicate 1 with 1.0 ng cDNA input
GSM2483290 Sample ERCC1 capture replicate 2 with 1.0 ng cDNA input
GSM2483291 Sample ERCC1 capture replicate 1 with 10.0 ng cDNA input
BioProject PRJNA374355
SRA SRP099258

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE94800_all_samples_molecule_counts.txt.gz 1.3 Mb (ftp)(http) TXT
GSE94800_cdna_mips_ase-K562-HEK293.txt.gz 4.3 Kb (ftp)(http) TXT
GSE94800_cdna_mips_ercc.txt.gz 25.5 Kb (ftp)(http) TXT
GSE94800_cdna_mips_geuvadis.txt.gz 6.1 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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