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Reason: The IDAT files are sensitive data and are available only upon request

Ex-vivo Drug Responses and Molecular Genetic Profiles of 597 Pediatric ALL Patients

dataset
posted on 2024-06-25, 12:51 authored by Anna Pia Enblad, Olga KraliOlga Krali, Josefine Palle, Kristin Blom, Claes AnderssonClaes Andersson, Britt-Marie Frost, Samppa Ryhänen, Trond Flaegstad, Ólafur G. Jónsson, Kjeld Schmiegelow, Mats Marshall HeymanMats Marshall Heyman, Arja Harila, Peter Nygren, Rolf Larsson, Gudmar Lönnerholm, Jessica NordlundJessica Nordlund

This dataset contains genome-wide DNA methylation data generated from 55 pediatric acute lymphoblastic leukemia (ALL) samples originating from bone marrow or peripheral blood samples taken at ALL diagnosis (n = 55).

Genome-wide DNA methylation was analyzed at the SNP&SEQ Technology Platform, SciLifeLab, National Genomics Infrastructure Uppsala, Sweden. Per sample, 250 ng of genomic DNA was bisulfite converted using EZ DNA MethylationTM Kit from Zymo Research. The bisulfite converted DNA was eluted in 15μl according to the manufacturer´s protocol, evaporated to a volume of <4μl, and used for methylation analysis using the Illumina Methylation EPICv2 array using the standard protocol from Illumina (iScan SQ instrument). This metadata record contains information about the raw IDAT files generated from the Infinium DNA methylation arrays. The raw IDAT files were processed with Genome Studio (V2011.1). Peak-based correction was used to normalize the beta-value matrix.

The following data will be made available upon request: i) the raw IDAT files, ii) a table with the unprocessed beta-values, signal intensities and detection p-values, iii) the processed beta-value matrix (peak-based corrected), iv) the CpG site annotation file and v) limited clinical information.


Terms for access

The DNA methylation dataset is only to be used for research that is seeking to advance the understanding of the influence of epigenetic factors on leukemia etiology and biology.

The data should not be used for other purposes, i.e. investigating the epigenetic signatures that may lead to identification of a person.

For retrieving the data used for the scope of this publication, please contact datacentre@scilifelab.se.

Funding

The Swedish Research Council (#2019-01976)

The Swedish Cancer Society (#CAN2022-2395)

The Swedish Childhood Cancer Foundation (#PR2022-0082)

History

Publisher

Uppsala University

Access request email

datacentre@scilifelab.se