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RNA-seq of SH-SY5Y NB cells stably transduced with shETV5 compared to parental cells, cell line samples and samples of xenografted tumors

Identifiers: SRA: ERP108798
BioProject: PRJEB26783
Center for Medical Genetics Ghent (CMGG) Cancer Research Institute Ghent (CRIG): E-MTAB-6713
Study Type: 
Transcriptome Analysis
Abstract: Stable ETV5 knockdown SH-SY5Y were used to investigate the role of ETV5 in vitro and in vivo. Libraries for mRNA sequencing were prepared using the TruSeq stranded mRNA sample prep kit (Illumina), involving polyA-selection, fragmentation, adapter ligation, reverse transcription and PCR amplification. Libraries were quantified using the Qubit 2.0 Fluorometer prior to sequencing with read length of 75 bp on a NextSeq 500 sequencer (Illumina). On average 24.7 M high-quality reads were generated per sample, with a minimal read count of 20.0 M reads for sample 2015_027_009 (sample L105). For each sample, gene-level read counts and KPKM-values were generated with Sailfish (Patro et al. 2014). Read counts are the number of reads overlapping a given feature such as a gene. KPKM-values (K-mers Per Kilobase of exon per Million reads) represent read counts normalized for sequencing depth and transcript length. KPKM-values allow you to compare genes across and within samples.
Description: Stable ETV5 knockdown SH-SY5Y were used to investigate the role of ETV5 in vitro and in vivo. Libraries for mRNA sequencing were prepared using the TruSeq stranded mRNA sample prep kit (Illumina), involving polyA-selection, fragmentation, adapter ligation, reverse transcription and PCR amplification. Libraries were quantified using the Qubit 2.0 Fluorometer prior to sequencing with read length of 75 bp on a NextSeq 500 sequencer (Illumina). On average 24.7 M high-quality reads were generated per sample, with a minimal read count of 20.0 M reads for sample 2015_027_009 (sample L105). For each sample, gene-level read counts and KPKM-values were generated with Sailfish (Patro et al. 2014). Read counts are the number of reads overlapping a given feature such as a gene. KPKM-values (K-mers Per Kilobase of exon per Million reads) represent read counts normalized for sequencing depth and transcript length. KPKM-values allow you to compare genes across and within samples.
External Link: E-MTAB-6713 in ArrayExpress

Related SRA data

Experiments:
15 ( 15 samples )
Runs:
180 (55.8Gbp; 23.8Gb)
Additional objects:
File type count
fastq 2