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| Status |
Public on Apr 28, 2024 |
| Title |
GTS slow 1 |
| Sample type |
SRA |
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| Source name |
non-seminoma germ cell tumor, growing teratoma
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| Organism |
Homo sapiens |
| Characteristics |
tissue: non-seminoma germ cell tumor, growing teratoma
group: GTS slow
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| Treatment protocol |
-
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| Growth protocol |
-
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated by the TRIzol reagent according to the manual (Qiagen, Hilden, Germany). RNA concentrations and purities were measured by the Nanodrop 2000 photo-spectrometer (260 / 280 nm; 260 / 230 nm) and RIN numbers were detemrined by Fragment Analyzer measurememt.
200 ng of total RNA were used for library preparation and microRNA sequencing (microRNAseg). Library preparation (NEXTFLEX Small RNA-Seq Kit v4‘ (Revvity, Hamburg, Germany)) and microRNAseg (NovaSeq6000 SP 2 x 50 bp) has been performed at the "Institut für Klinische Molekularbiologie" (IKMB) of the University of Kiel. The quality control (QC) and identification of expressed microRNAs has been done by the IKMB.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Demultiplexing was done with bcl2fastq v2.20.0.422. Analysis was performed using ‘nf-core/smrnaseq v2.2.0‘, against the human reference genome GRCh38. The statistical QC was performed using the FastQC tool. (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), generating the mean quality scores of all sequences, sequence duplication levels and the count of unique / duplicate reads. Counts per million were calculated by the TMM normalization method in the edgeR package
Assembly: GRCh38
Supplementary files format and content: Excel data, showing expression intensities of each analyzed microRNA. Values are averaged from 2x paired-end sequening runs performed for each sample.
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| Submission date |
Dec 23, 2023 |
| Last update date |
Apr 28, 2024 |
| Contact name |
Daniel Nettersheim |
| Organization name |
Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University
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| Department |
Dep. of Urology
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| Lab |
Urological Research Laboratory, Translational UroOncology
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| Street address |
Moorenstr. 5
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| City |
Düsseldorf |
| State/province |
NRW |
| ZIP/Postal code |
40225 |
| Country |
Germany |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE251975 |
MicroRNA sequencing of growing teratoma tissues |
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| Relations |
| BioSample |
SAMN39093283 |
| SRA |
SRX23011109 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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