GEO DataSets

(Submitter supplied) Expression profiling of a panel of 101 adult male germ cell tumors and 5 normal testis specimens was performed on Affymetrix U133A and U133B microarrays. This data has been used to: 1) generate a gene classifier that predicts histology (see PMID 15870693). 2) identify candidate target genes on 12p, a region that is gained in almost 100% of germ cell tumors (see PMID 16424014) 3) identify pluripotency associated genes through comparison of pluripotent embryonal carcinoma vs. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL96 GPL97

214 Samples

Download data: CEL, EXP

(Submitter supplied) The predominant view of pluripotency regulation proposes a stable ground state with coordinated expression of key transcription factors (TFs) that prohibit differentiation. Another perspective suggests a more complexly regulated state involving competition between multiple lineage-specifying TFs that define pluripotency. These contrasting views were developed from extensive analyses of TFs in pluripotent cells in vitro. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18723

8 Samples

Download data: TXT

(Submitter supplied) This series represents expression profiles of 34 non-seminoma germ cell tumors (NSGCTs) from patients who received cisplatin based chemotherarpy for treatment of their disease for whom full clinical follow-up information was available. These specimens were used as a validation set to test outcome prediction models using a subset of previously profiled GCT specimens (see GEO accession #GSE3218). Keywords: Disease state analysis (good vs. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL97 GPL96

68 Samples

Download data: CEL, EXP

(Submitter supplied) Genomic profiling of a panel of 74 adult male germ cell tumors of various histologies from primary and metastatic sites using high resolution BAC array CGH. See Pubmed ID # 17943972. Completed Study: Statistical analyses were performed to identify regions that were frequently altered in all tumors, as well as in specific histologic subsets and from different tumor sites (i.e., primary gonadal, primary extra-gonadal, and metastatic). more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL5679

74 Samples

Download data: GPR

(Submitter supplied) Normal, premalignant and various histological subtypes of testicular germ cell tumor (TGCT) tissues were hybridized against Universal Human Reference RNA (Stratagene) onto Agilent 60mer oligo microarrays (GEO accession no GPL885). In vitro time series of two TGCT cell lines, NTERA2 and 2102Ep, treated with retinoic acid for 0, 3, and 7 days were also included. The data set (30 hybridizations) is particularly useful for comparisons between various histological subtypes of TGCT versus each other or versus normal testis. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL885

30 Samples

Download data: TIFF

(Submitter supplied) NT2 cells were treated with DMSO (control) or 10uM Retinoic Acid (RA). Total RNA was isolated using TriReagent, and subsequent cleanup with RNeasy columns (Qiagen) according to the manufacturer's directions. Hybridizations were performed according to Affymetrix guidelines using the Human HG-U133A chip containing 22,500 unique genetic elements. Double-stranded cDNA was synthesized using Superscript II RT (Invitrogen). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

2 Samples

Download data

(Submitter supplied) We hypothesized that the comparison between pure type seminoma and seminoma components in mixed tumor (mixed type seminoma) could reveal early changes of the reprogramming process; however, only a little data is available. We performed gene expression microarray analysis of 6 pure type and 6 mixed type seminomas, and the hierarchical clustering analysis properly grouped each type of seminomas into a separated cluster. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL20844

12 Samples

Download data: TXT

(Submitter supplied) Illumina Infinium MethylationEPIC BeadChip (850k) array analysis of DNA methylation of embryonal carcinoma cell lines NCCIT and 2102EP deficient for CD24 and parental cells. CD24 deficiency was genereted by CRISPR/Cas9 method. Three different NCCIT and 2102EP knock out clones were analyzed.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL23976

8 Samples

Download data: IDAT, XLSX

(Submitter supplied) Single eng 3' RNA sequencing of embryonal carcinoma cell line NCCIT deficient for CD24 and parental cells. CD24 deficiency was genereted by CRISPR/Cas9 method. Five different NCCIT knock out clones were sequenced.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21290

7 Samples

Download data: XLSX

(Submitter supplied) Illumina 450k DNA methylation microarray analysis of seminoma-like TCam-2 cells xenografted in nude mice. 2120EP embryonal carcinoma cells served as control. TCam-2 cells acquire pluripotency and become epigenetically reprogrammed to an embryonal carcinoma-like state during in vivo growth. This analysis is part of the article 'BMP inhibition in seminomas initiates acquisition of pluripotency via NODAL signaling resulting in reprogramming to an embryonal carcinoma' by Nettersheim et al., 2015. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

12 Samples

Download data: TXT

(Submitter supplied) Illumina expression microarray analysis of seminoma-like TCam-2 cells xenografted in nude mice. 2120EP embryonal carcinoma cells served as control. TCam-2 cells acquire pluripotency and become epigenetically reprogrammed to an embryonal carcinoma-like state during in vivo growth. This analysis is part of the article 'BMP inhibition in seminomas initiates acquisition of pluripotency via NODAL signaling resulting in reprogramming to an embryonal carcinoma' by Nettersheim et al., 2015. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

12 Samples

Download data: TXT

(Submitter supplied) Comparison of miRNA expression profiles in malignant germ cell tumors compared to non-malignant control group. Use of bioinformatic algorithm Sylamer to interrogate mRNA expression profiles from malignant germ cell tumors for enrichment or depletion of binding sites for differentially expressed miRNAs. Use of Gene Ontology (GO) analysis to demonstrate functional significance of differentially expressed miRNAs in malignant germ cell tumors.

Organism:

Betapolyomavirus macacae; JC polyomavirus; Human immunodeficiency virus 1; Merkel cell polyomavirus; Human alphaherpesvirus 1; Human alphaherpesvirus 2; Lymphocryptovirus; Homo sapiens; Human betaherpesvirus 5; Rhadinovirus; Betapolyomavirus hominis

Type:

Expression profiling by array; Non-coding RNA profiling by array; Third-party reanalysis

Platforms:

GPL9957 GPL96

94 Samples

Download data: CEL, TXT

(Submitter supplied) Remarkably little is known about the transcriptional profiles of human embryonic stem (ES) cells or the molecular mechanisms that underlie their pluripotency. To identify commonalties among the transcriptional profiles of different human pluripotent cells and to search for clues into the genesis of human germ cell tumors, we compared the expression profiles of human ES cell lines, human germ cell tumor cell lines and tumor samples, somatic cell lines, and testicular tissue samples by using cDNA microarray analysis. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

8 related Platforms

74 Samples

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(Submitter supplied) To compare the transcriptome profiles of the two principal histological variants of malignant germ cell tumor that occur in childhood Keywords: Disease state analysis

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS3262

Platform:

GPL96

27 Samples

Download data: CEL

Analysis of yolk sac tumors (YSTs) and seminomas, the two principal histological variants of pediatric malignant germ cell tumors (MGCTs). Seminomas and YSTs are presumed to arise from the same progenitor cell. Results provide insight into the molecular basis for the divergence of pediatric MGCTs.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 2 disease state sets

Platform:

GPL96

Series:

GSE10615

27 Samples

Download data: CEL

(Submitter supplied) Malignant (type II) testicular germ cell tumors (TGCT) are considered tumors of embryonic germ cell ancestry that diverge morphologically as seminoma (SE), and nonseminomas (NS), the latter including embryonal carcinoma (EC), teratoma (TE), yolk sac tumor (YS) and choriocarcinoma. We have analyzed the genomes and epigenomes of pure histological forms of TGCT (n=130) and 128 matched adjacent normal testicular tissues for TGCT core and subtype-specific DNA methylome profiles and somatic copy number aberrations (SCNA). more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

267 Samples

Download data: TXT

(Submitter supplied) Illumina expression microarray analysis of seminoma-like TCam-2 cells depleted for SOX2 by CRISPR/Cas9. Cells were xenografted in nude mice. 2120EP embryonal carcinoma and parental TCam-2 cells were xenograted as controls. Tumors were recovered after 1 (1w) and 6 weeks (clone 1 - 5) of in vivo growth. Additionally, in vitro cultivated TCam-2 were analyzed as control. The data set is part of the study 'SOX2 is essential for in vivo reprogramming of seminoma-like TCam-2 cells to an embryonal carcinoma-like fate' (Nettersheim et al., 2016, Oncotarget).

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

9 Samples

Download data: TXT

(Submitter supplied) Genomic screening was performed for one family containing MZ twins with testicular germ cell tumors, in order to define alterations associated with risk of tumor development.

Organism:

Homo sapiens

Type:

Genome variation profiling by array; Genome variation profiling by high throughput sequencing

Platform:

GPL8841

6 Samples

Download data: TXT

(Submitter supplied) Dmrt1 (doublesex and mab-3 related transcription factor 1) is a conserved transcriptional regulator of male differentiation required for testicular development in vertebrates. In mice of the 129Sv strain, loss of Dmrt1 causes a high incidence of teratomas. Mutant 129Sv germ cells undergo apparently normal differentiation up to embryonic day 13.5 (E13.5), but some cells fail to arrest mitosis and ectopically express pluripotency markers. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

6 Samples

Download data: CEL

(Submitter supplied) Very recently, a number of independent studies showed that serum levels of embryonic micro-RNA (miR) clusters 371-3 and 302abc/367 are predictive for the presence of testicular type II germ cell tumors. These miRs could be used to sensitively detect SE and EC components which are indeed known to express these miRs [1-7]. This study investigates ca 750 miRs in a high throughput approach to validate these previously identified markers and identify novel potential miR markers for testicular type II germ cell tumors. more...

Organism:

Homo sapiens

Type:

Expression profiling by RT-PCR

Platform:

GPL18971

35 Samples

Download data: TXT