![](/coreweb/template1/pix/main_left_bg.gif) |
![](/coreweb/template1/pix/pixel.gif) |
GEO help: Mouse over screen elements for information. |
|
Status |
Public on Apr 28, 2024 |
Title |
GTS rapid 2 |
Sample type |
SRA |
|
|
Source name |
non-seminoma germ cell tumor, growing teratoma
|
Organism |
Homo sapiens |
Characteristics |
tissue: non-seminoma germ cell tumor, growing teratoma group: GTS rapid
|
Treatment protocol |
-
|
Growth protocol |
-
|
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.
|
|
|
Library strategy |
miRNA-Seq |
Library source |
transcriptomic |
Library selection |
size fractionation |
Instrument model |
Illumina NovaSeq 6000 |
|
|
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.
|
|
|
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
|
Department |
Dep. of Urology
|
Lab |
Urological Research Laboratory, Translational UroOncology
|
Street address |
Moorenstr. 5
|
City |
Düsseldorf |
State/province |
NRW |
ZIP/Postal code |
40225 |
Country |
Germany |
|
|
Platform ID |
GPL24676 |
Series (1) |
GSE251975 |
MicroRNA sequencing of growing teratoma tissues |
|
Relations |
BioSample |
SAMN39093279 |
SRA |
SRX23011113 |
Supplementary data files not provided |
SRA Run Selector![Help](/coreweb/images/long_help4.gif) |
Raw data are available in SRA |
|
|
|
|
![](/coreweb/template1/pix/main_right_bg.gif) |