|
| Status |
Public on Jun 03, 2015 |
| Title |
PRDM12 mutant male E172D |
| Sample type |
SRA |
| |
|
| Source name |
PRDM12 mutant fibroblasts
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: skin
cell type: fibroblasts
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified using RNAeasy mini Kit (Qiagen). poly-T selected RNA was isolated and dUTP-containing cDNA was generated.
Illumina TruSeq protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
50-bp single-end Illumina mRNA sequencing reads were aligned using Tophat v2.0.10 and bowtie v0.12.9.
aligned reads were counted with HTSeq
FPKM estimation was performed with Cufflinks (v2.1.1) and differential expression analysis with DESeq2 (v1.2.10)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample (standard output cufflinks)
|
| |
|
| Submission date |
Sep 22, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Vanja Nagy |
| Organization name |
IMBA - Institute of Molecular Biotechnology GmbH
|
| Street address |
Dr. Bohr-Gasse 3
|
| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE61600 |
Comparison of human PRDM12 mutants D31Y and E172D with wildtype fibroblasts |
|
| Relations |
| BioSample |
SAMN03075319 |
| SRA |
SRX707567 |
