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Data released on November 26, 2015

Supporting data for "Multi-platform microRNA profiling of hepatoblastoma patients using formalin fixed paraffin embedded archival samples".

Chatterjee, A; Eccles, M, R; Leichter, A, L; Purcell, R, V; Sullivan, M, J (2015): Supporting data for "Multi-platform microRNA profiling of hepatoblastoma patients using formalin fixed paraffin embedded archival samples". GigaScience Database. http://dx.doi.org/10.5524/100180 RIS BibTeX Text

Formalin fixed paraffin embedded (FFPE) samples are a valuable resource in cancer research and have the potential to be extensively used. However, they are often underused because of degradation and chemical modifications occurring in the RNA that can present obstacles in downstream analysis. In routine medical care, FFPE material is examined and archived, therefore clinical collections of many types of cancers exist. It is beneficial to assess and record the quality of data that can be obtained from this type of material. The current study investigated three independent platforms and their ability to profile microRNAs (miRNAs) within FFPE samples from hepatoblastoma (HB) patients. Here we present three types of dataset consisting of miRNA profiles for 13 HB patients with different tumour types and molecular variations. The three platforms that were used to generate these data are: next-generation sequencing (Illumina MiSeq), microarray (Affymetrix® GeneChip® miRNA 3.0 array) and NanoString (nCounter, Human v2 miRNA Assay). The mature miRNAs identified are based on miRBase version 17 and 18. These datasets provide a global landscape of miRNA expression for a rare childhood cancer that has not previously been well characterised. These data could serve as a resource for future studies aiming to make comparisons of HB miRNA profiles and to document aberrant miRNA expression in this type of cancer.

Contact Submitter

Related manuscripts:

doi:10.1186/s13742-015-0099-9

Accessions (data included in GigaDB):

GEO: GSE62010
GEO: GSE62011
GEO: GSE62017

Keywords:

miRNA FFPE RNA expression Microarray Next-generation sequencing NanoString Hepatoblastoma Epigenetics 

Transcriptomic, Epigenomic

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Funding:

  • Funding body - Children's Cancer Research Fund

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
S109606HumanhumanHomo sapiens Age:1.5
Tissue type:Epithelial
Description:Fetal/embryonal Surgical specimen (pos...
...
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S119606HumanhumanHomo sapiens Age:0.67
Tissue type:Epithelial
Description:Fetal Surgical specimen (post-chemo)
...
+
S129606HumanhumanHomo sapiens Age:1.92
Tissue type:Epithelial/mesenchymal
Description:Fetal/embryonal Surgical specimen (pos...
...
+
S139606HumanhumanHomo sapiens Age:2.33
Tissue type:Epithelial
Description:Fetal Surgical specimen (post-chemo)
...
+
S149606HumanhumanHomo sapiens Age:0.5
Tissue type:Epithelial
Description:Fetal/embryonal Surgical specimen (pos...
...
+
S159606HumanhumanHomo sapiens Age:2.08
Tissue type:Epithelial
Description:Fetal Surgical specimen (post-chemo)
...
+
S169606HumanhumanHomo sapiens Age:0.33
Tissue type:Epithelial
Description:Fetal Surgical specimen (post-chemo)
...
+
S49606HumanhumanHomo sapiens Age:2
Tissue type:Epithelial/mesenchymal
Description:Fetal Surgical specimen (post-chemo)
...
+
S59606HumanhumanHomo sapiens Age:0.42
Tissue type:Epithelial
Description:Fetal Surgical specimen (post-chemo)
...
+
S69606HumanhumanHomo sapiens Age:0.67
Tissue type:Epithelial
Description:Fetal Surgical specimen (post-chemo)
...
+
Displaying 1-10 of 13 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile TypeFile FormatSizeRelease Date 
OtherEXCEL34.72 KB2015-11-17
OtherEXCEL34.28 KB2015-11-17
OtherEXCEL71.69 KB2015-11-17
OtherEXCEL75.21 KB2015-11-17
OtherEXCEL51.38 KB2015-11-17
OtherEXCEL198.22 KB2015-11-17
OtherEXCEL99.59 KB2015-11-17
Displaying 1-7 of 7 File(s).

History:

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