|
| Status |
Public on Mar 23, 2020 |
| Title |
Nontumor3 |
| Sample type |
SRA |
| |
|
| Source name |
Normal liver tissue
|
| Organism |
Homo sapiens |
| Characteristics |
disease diagnosis: Hepatoblastoma
tissue: Normal liver tissue
sample type: Nontumor
gender: Male
patient: 3
|
| Extracted molecule |
total RNA |
| Extraction protocol |
20mg of frozen tissue was homogenized with FASTprep. RNA was extracted using the MirVana kit (Thermofisher) and subsequently treated with DNase (kit DNA free kit, Thermofisher) following manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
NT3
processed data file: RNAseq_counts_32patients.txt
|
| Data processing |
STAR alignment to hg38.
gatk to generate filtered vcf.
Filter SNPs.
Filter ALUs, seq biases.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: RNAseq_counts_32patients.txt: Tab-delimited text file containing the table counts.
|
| |
|
| Submission date |
Jun 19, 2019 |
| Last update date |
Mar 23, 2020 |
| Contact name |
Carolina Armengol |
| E-mail(s) |
carmengol@igtp.cat
|
| Phone |
+34670799690
|
| Organization name |
Germans Trias i Pujol Health Research Institute
|
| Street address |
Crta Can Ruti; cami de les escoles, S/N
|
| City |
Badalona |
| State/province |
Barcelona |
| ZIP/Postal code |
08916 |
| Country |
Spain |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE132219 |
Epigenetic footprint of hepatoblastoma defines a novel integrative molecular classification with clinical implications |
| GSE133039 |
Epigenetic footprint of hepatoblastoma defines a novel integrative molecular classification with clinical implications [RNA-seq] |
|
| Relations |
| BioSample |
SAMN12097079 |
| SRA |
SRX6095857 |
