ACGH in paired blood/tumor samples in Wilms Tumors
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE69971 | GEO | 2015/06/19
SECONDARY ACCESSION(S): PRJNA287427
REPOSITORIES: GEO
Similar Datasets
Project description:Array CGH analysis of paired blood and tumor DNA samples from 14 patients with sporadic Wilms tumor. Previously array CGH studies in WT have only been performed in tumor tissue samples. We herein describe a novel set of constitutional abnormalities and point to candidate genes that might be associated with WT development. 28 paired DNA samples of peripheral blood/fresh tumor tissue from 14 patients (10 males, 4 females) with histologically confirmed WT. All tumor samples were collected from primary tumors from patients treated with the same neoadjuvant chemotherapy following the International Society of Paediatric Oncology (SIOP) WT 2001 trial protocol.
2015-06-19 | E-GEOD-69971 | biostudies-arrayexpress
Project description:Wilms tumor (WT) is the most common renal malignancy in children. So we aim to investigate the transcriptomic map of Wilms tumor.
2022-05-18 | GSE138869 | GEO
Project description:Genome-wide DNA copy number was studied to determine whether the Wilms' tumor samples generally show normal copy number variation comparing to the colon tumor samples We used custom Nimblegen microarrays to determine the genome-wide DNA copy number in human Wilms' Tumor samples
2011-08-29 | GSE29374 | GEO
Project description:The aim of this study is to discover loss of specific miRNA loci in Wilms' tumors using array CGH. Custom arrays were designed based on the Agilent 2x105K Human Whole Genome Genomic microarray with Agilent’s eArray program (https://earray.chem.agilent.com/earray/), with additional probes that cover all miRNA regions (200 bps before, within and after each miRNA from miRBase v13, with each probe in triplicates to enhance the reliability). All custom-designed probes were designed in UCSC hg18. Probes from Agilent’s database were lifted-over from hg19 to hg18 (LiftOver tool: http://genome.ucsc.edu). The Agilent 2x105K custom-design whole genome microarray was used to analyze genomic alterations in Wilms' tumor samples compared to normal human genomic DNA (Promega p/n G1523).
2012-03-30 | E-GEOD-28397 | biostudies-arrayexpress
Project description:Paired whole genome sequencing tumor normal samples of pediatric Wilms tumors
| EGAS00001006526 | EGA
Project description:Purpose: Bulk transcriptomics analysis of Wilms tumor SIX2+CITED1+ cells to compare and identify unique nephron progenitor transcriptome profiling (RNA-seq) signature between unfavorable and favorable Wilms Tumors and against human fetal kidney Methods: Wilms tumor samples were collected and transported on ice at 4°C in RPMI-1640 and a single cell suspensions were prepared following mechanical and enzymatic dissociation as previously publication. Enzymatic dissociation was performed with 125 U/ml collagenase I in RPMI-1640 at 37 °C for 35 min. The digested cells were then passed through a 100-μm cell strainer and a 40-μm cell strainer with washes of 1x PBS. The cell suspension was than centrifuged at 1500 rpm for 5 min and erythrocytes were eliminated using a red blood cell lysis kit. WT SIX2+CITED1+ cells were isolated using SIX2-Cy5 and CITED1-Cy3 Smartflare RNA probes following manufacturer’s instructions and previous publication. Briefly, cells were incubated over night at 37 °C with both RNA probes diluted at 1:20 in PBS and 25ul/ml in RPMI-1640 supplemented with 5% FBS, and 0.2% antimicrobial agent Primocin. After 16-18 h, cells were dissociation using TrypLE 1x for 5 min, cells were centrifuged at 1500 rpm for 5 min and prepared for FACS. RNA extraction was performed immediately after FACS using the RNeasy Micro Kit following manufacturer’s recommendations. After cDNA production and construction of DNA libraries, the samples were run on an Illumina NextSep500 (Illumina). Differential gene expression was analyzed using ERCC ExFold probes with the Remove Unwanted Variation R/Bioconductor software package combined with edgeR Results: Transcriptomics analysis of Wilms Tumor SIX2+CITED1+ cells in comparison to different tumor types and human fetal kidneys confirmed the nephrogenic signature of hFK-SIX2+CITED1+ and WT-SIX2+CITED1+ cells but highlighted differences in expression of pluripotency and self renewal-related genes like OCT4, FOXO1, SALL, NANOG along with a lower expression of β-catenin, TCF, and other growth factors known to promote differentiation (BMPs, FGFs). Hierarchical clustering of gene expression showed shared similarities between Wilms tumor samples against human fetal kidney samples however, with major differences in gene expression between tumor-to-tumor type was also present. Conclusion: Our study represents the first transcriptomic characterization of Wilms Tumor cancer stem cells (SIX2+CITED1+) against human fetal kidney SIX2+CITED1+ cells. Identifying specify gene expression and signaling pathway profiles across different subtypes of Wilms Tumor and against human fetal kidney SIX2+CITED1+ cells.
2024-01-08 | GSE176342 | GEO
Project description:Abstract: Background: MiRNA signatures in human sera have been reported for various tumor diseases. Here we generated miRNA profiles analyzing 1205 mature miRNA transcripts of serum samples of Wilms tumor patients, taken prior and after chemotherapy according to SIOP protocol 2001. Using a feature subset selection filter approach we identified a minimal number of miRNAs with a maximum contribution for the classification between treated and untreated patients and between patients and controls. Results: Analyzing 1205 mature miRNAs, we separated controls and Wilms tumor patients prior chemotherapy with an accuracy of 0.81. We obtained a similar accuracy (0.82) for the separation between controls and sera of Wilms tumor patients after preoperative chemotherapy. We identified 23 miRNAs that were differentially expressed in both comparisons. Subset selection improved the overall classification accuracy between controls and Wilms tumor patients prior and after chemotherapy to 0.94 and 0.91, respectively. Subset selection also allowed separating between Wilms tumor patients prior and after chemotherapy with an accuracy of 0.98. Conclusion: Our analysis identified serum based miRNA signatures that allowed separating between controls, untreated Wilms tumor patients, and Wilms tumor patients after chemotherapy with high accuracy for each of these comparisons.
2014-12-31 | GSE48137 | GEO
Project description:The aim of the study was to identify differentially expressed mRNAs in different Wilms tumor subtypes and correlate them to miRNA expression profiles of the same tumor samples.
2016-05-11 | GSE66405 | GEO
Project description:The IGF2-intronic miR-483 selectively enhances transcription from IGF2 fetal promoters and enhances tumorigenesis. The expression levels of microRNAs were profiled in 20 human Wilms tumor samples (WT), 3 human normal adult kidney samples (AK) and 5 human fetal kidney samples (FK) using a Luminex bead platform.
2013-12-22 | E-GEOD-50505 | biostudies-arrayexpress