|
| Status |
Public on Jun 21, 2017 |
| Title |
Fes KO – repl 4 |
| Sample type |
SRA |
| |
|
| Source name |
Fes KO, melanoma
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Melanoma
genotype/variation: Fes KO
|
| Treatment protocol |
Topical treatment on the back skin with 5 mM 4OH-Tamoxifen
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extracted using RNeasy Mini kit (Qiagen) following manufacturer’s instructions. The RNA quality was assessed using Bioanalyzer’s RNA nanochip (Agilent) and RNA with RIN values >7 were used for library preparation.
RNA libraries prepared using Illumina’s NextSeq library prep kit (Illumina) and library quality confirmed on Bioanalyzer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
15-674
|
| Data processing |
Samples sequenced on Illumina NextSeq 500 High 75 generating on average 19.8 million reads per sample.
FastQC was used to assess the quality of the sequenced data
Raw reads mapped to the mouse reference genome (mm10) using STAR (version 2.51b)
Reads assigned to Ensembl genes (GRCm38.84) and counted using Subread (version 1.4.6)
Genome_build: mm10
Supplementary_files_format_and_content: [RNAseq_counts.txt] Tab-delimited text file including mapped counts.
Supplementary_files_format_and_content: [RNAseq_SFnorm_log2_counts.txt] Tab-delimited text file including log2 size-factor normalized counts.
|
| |
|
| Submission date |
Jun 21, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Sara Aibar |
| Organization name |
VIB-KU Leuven
|
| Department |
Center for Brain & Disease Research
|
| Lab |
Laboratory of Computational Biology
|
| Street address |
Herestraat 49
|
| City |
Leuven |
| ZIP/Postal code |
3001 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE83580 |
RNA-sequencing of Fes KO and WT melanomas |
|
| Relations |
| BioSample |
SAMN05277815 |
| SRA |
SRX1868829 |
