Supporting material for: Paediatric Leukaemia DNA methylation profiling using MBD enrichment and SOLiD Sequencing on archival bone marrow smears.

Dataset type: Genomic
Data released on March 09, 2015

Wong NCL; Meredith GD; Marnellos G; Dudas M; Parkinson-Bates M; Halemba MS; Chatterton Z; Maksimovic J; Ashley DM; Mechinaud F; Craig JM; Saffery R (2015): Supporting material for: Paediatric Leukaemia DNA methylation profiling using MBD enrichment and SOLiD Sequencing on archival bone marrow smears. GigaScience Database. http://dx.doi.org/10.5524/100099

DOI10.5524/100099

Acute Lymphoblastic Leukaemia(ALL) is the most common cancer in children. Over the past four decades, research has advanced the treatment of this cancer from less than 60% chance of survival to over 85% today. The causal molecular mechanisms remain unclear. We performed SOLiD sequencing on Methyl-Binding Domain(MBD) enriched fractions of genomic DNA from eight paediatric ALL patients using archived bone marrow smear microscope slides. Primary tumour and remission bone marrow sample was analysed. Four patients relapsed and the relapsed tumour was analysed. Input and MBD-enriched DNA from each sample was sequenced, aligned to the hg19 reference genome and analysed for enrichment peaks using MACS and HOMER. In total, 3.67Gb were sequenced, 2.74Gb were aligned to the reference genome (average 74.66% alignment efficiency). Our dataset represents one of the first SOLiD MBD-Seq studies performed on paediatric ALL and is the first to utilise archival bone marrow smears.

Additional details

Read the peer-reviewed publication(s):

Wong, N. C., Meredith, G. D., Marnellos, G., Dudas, M., Parkinson-Bates, M., Halemba, M. S., … Saffery, R. (2015). Paediatric leukaemia DNA methylation profiling using MBD enrichment and SOLiD sequencing on archival bone marrow smears. GigaScience, 4(1). doi:10.1186/s13742-015-0050-0





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
bm10_cd19-E9606HumanhumanHomo sapiens Age:not available
Analyte type:DNA
Experimental factor:MBD-enriched fraction
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bm10_cd19-I9606HumanhumanHomo sapiens Age:not available
Analyte type:DNA
Experimental factor:MBD-input fraction
...
+
bm10_cd33-E9606HumanhumanHomo sapiens Age:not available
Analyte type:DNA
Experimental factor:MBD-enriched fraction
...
+
bm10_cd33-I9606HumanhumanHomo sapiens Age:not available
Analyte type:DNA
Experimental factor:MBD-input fraction
...
+
bm10_cd34-E9606HumanhumanHomo sapiens Age:not available
Analyte type:DNA
Experimental factor:MBD-enriched fraction
...
+
bm10_cd34-I9606HumanhumanHomo sapiens Age:not available
Analyte type:DNA
Experimental factor:MBD-input fraction
...
+
bm10_cd45-E9606HumanhumanHomo sapiens Age:not available
Analyte type:DNA
Experimental factor:MBD-enriched fraction
...
+
bm10_cd45-I9606HumanhumanHomo sapiens Age:not available
Analyte type:DNA
Experimental factor:MBD-input fraction
...
+
bm9_cd19-E9606HumanhumanHomo sapiens Age:not available
Analyte type:DNA
Experimental factor:MBD-enriched fraction
...
+
bm9_cd19-I9606HumanhumanHomo sapiens Age:not available
Analyte type:DNA
Experimental factor:MBD-input fraction
...
+
Displaying 1-10 of 80 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
DirectoryUNKNOWN1.4 GB2015-01-21
TextTEXT0.04 KB2015-01-21
Leu135-E +AlignmentsBIGWIG695.01 MB2015-01-21
TextTEXT0.09 KB2015-01-21
OtherTrackDB0.9 KB2015-01-21
DirectoryUNKNOWN994 MB2015-01-21
TextTEXT0.04 KB2015-01-21
Rem135-E +AlignmentsBIGWIG492.67 MB2015-01-21
AnnotationTEXT0.09 KB2015-01-21
OtherTrackDB0.89 KB2015-01-21
Displaying 1-10 of 40 File(s).
Date Action
April 27, 2015 Manuscript Link added : 10.1186/s13742-015-0050-0