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Data from: Transcriptomic analysis reveals pro-inflammatory signatures associated with acute myeloid leukemia progression

dataset
posted on 08.10.2021, 10:04 by Linda HolmfeldtLinda Holmfeldt, Svea Stratmann

Data Set Description


These data are collected from a total of 70 participants (47 adult; 23 pediatric), all of which had relapsed or primary resistant acute myeloid leukemia. The data, which here are separated into an adult and a pediatric dataset, were generated as part of a study by Stratmann et. al. (https://doi.org/10.1182/bloodadvances.2021004962). The Stratmann et. al. study is currently pre-published here: https://ashpublications.org/bloodadvances/article/doi/10.1182/bloodadvances.2021004962/477210/Transcriptomic-analysis-reveals-pro-inflammatory

Please note that separate applications are necessary for the adult and pediatric dataset, respectively. When applying for access, please indicate which of the datasets that the application applies for.

The adult dataset contains transcriptome sequencing (RNA-seq) data from 25 diagnosis (D), 45 relapse (R1/R2/R3) and five (5) primary resistant (PR) leukemic samples from 47 patients, as well as five (5) normal CD34+ bone marrow control samples.

The pediatric dataset contains RNA-seq data from 18 diagnosis (D), 22 relapse (R1/R2), six (6) persistent relapse (R1/2-P) and one (1) primary resistant (PR) leukemic samples from 23 patients, as well as five (5) normal CD34+ bone marrow control samples.

The leukemic samples originate from bone marrow or peripheral blood. The normal RNA samples originate from purified CD34+ bone marrow cells from five different healthy individuals. Further details regarding the samples are available in the Supplemental Information part of Stratmann et. al. (https://doi.org/10.1182/bloodadvances.2021004962).

RNA-seq libraries and associated next-generation sequencing were carried out by the SNP&SEQ Technology platform, SciLifeLab, National Genomics Infrastructure Uppsala, Sweden. Libraries were prepared using the TruSeq stranded total RNA library preparation kit with ribosomal depletion by RiboZero Gold (Illumina). Sequencing of adult samples was carried out on the Illumina HiSeq2500 platform, generating paired-end 125bp reads using v4 sequencing chemistry. Sequencing of pediatric samples was carried out on the Illumina NovaSeq6000 platform (S2 flowcell), generating paired-end 100bp reads using the v1 sequencing chemistry. The CD34+ bone marrow control samples were sequenced using both platforms (Illumina HiSeq2500 and NovaSeq6000).

Further, all of these acute myeloid leukemia samples have also been characterized by whole genome sequencing or whole exome sequencing, with the datasets available under controlled access through doi.org/10.17044/scilifelab.12292778.

Terms for access

The adult and pediatric datasets are only to be used for research that is seeking to advance the understanding of the influence of genetic and transcriptomic factors on human acute myeloid leukemia etiology and biology.

Use of the protected pediatric dataset is only for research projects that can merely be conducted using pediatric acute myeloid leukemia data, and for which the research objectives cannot be accomplished using data from adults. Applications intending various method development would thus not be considered as acceptable for use of the pediatric dataset. Further, the pediatric dataset may not be used for research investigating predisposition for acute myeloid leukemia based on germline variants.

For conditional access to the adult and/or pediatric dataset in this publication, please contact datacentre@scilifelab.se

Funding

Knut and Alice Wallenberg Foundation (KAW 2013-0159)

The Swedish Research Council (2013-03486)

The Swedish Cancer Society (CAN2013/489)

The Swedish Childhood Cancer Foundation (PR2013-0070)

The Kjell and Märta Beijer Foundation

History

Publisher

Uppsala Universitet

Access request email

datacentre@scilifelab.se