Dataset Information

Genomic, transcriptomic and epigenomic sequencing data of the B-cell leukemia cell line REH.

ABSTRACT:

Objectives

The aim of this data paper is to describe a collection of 33 genomic, transcriptomic and epigenomic sequencing datasets of the B-cell acute lymphoblastic leukemia (ALL) cell line REH. REH is one of the most frequently used cell lines for functional studies of pediatric ALL, and these data provide a multi-faceted characterization of its molecular features. The datasets described herein, generated with short- and long-read sequencing technologies, can both provide insights into the complex aberrant karyotype of REH, and be used as reference datasets for sequencing data quality assessment or for methods development.

Data description

This paper describes 33 datasets corresponding to 867 gigabases of raw sequencing data generated from the REH cell line. These datasets include five different approaches for whole genome sequencing (WGS) on four sequencing platforms, two RNA sequencing (RNA-seq) techniques on two different sequencing platforms, DNA methylation sequencing, and single-cell ATAC-sequencing.

SUBMITTER: Lysenkova Wiklander M

PROVIDER: S-EPMC10566058 | biostudies-literature | 2023 Oct

REPOSITORIES: biostudies-literature

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Publications

Genomic, transcriptomic and epigenomic sequencing data of the B-cell leukemia cell line REH.

Lysenkova Wiklander Mariya M Övernäs Elin E Lagensjö Johanna J Raine Amanda A Petri Anna A Wiman Ann-Christin AC Ramsell Jon J Marincevic-Zuniga Yanara Y Gezelius Henrik H Martin Tom T Bunikis Ignas I Ekberg Sara S Erlandsson Rikard R Larsson Pontus P Mosbech Mai-Britt MB Häggqvist Susana S Hellstedt Kerje Susanne S Feuk Lars L Ameur Adam A Liljedahl Ulrika U Nordlund Jessica J

BMC research notes 20231010 1

<h4>Objectives</h4>The aim of this data paper is to describe a collection of 33 genomic, transcriptomic and epigenomic sequencing datasets of the B-cell acute lymphoblastic leukemia (ALL) cell line REH. REH is one of the most frequently used cell lines for functional studies of pediatric ALL, and these data provide a multi-faceted characterization of its molecular features. The datasets described herein, generated with short- and long-read sequencing technologies, can both provide insights into ...[more]

PMID: 37817248

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Project description:BackgroundPsychiatric disorders such as schizophrenia (SZ) and bipolar disorder (BP) are projected to lead the global disease burden within the next decade. Several lines of evidence suggest that epigenetic- or genetic-mediated dysfunction is frequently present in these disorders. To date, the inheritance patterns have been complicated by the problem of integrating epigenomic and transcriptomic factors that have yet to be elucidated. Therefore, there is a need to build a comprehensive database for storing epigenomic and transcriptomic data relating to psychiatric disorders.DescriptionWe have developed the PD_NGSAtlas, which focuses on the efficient storage of epigenomic and transcriptomic data based on next-generation sequencing and on the quantitative analyses of epigenetic and transcriptional alterations involved in psychiatric disorders. The current release of the PD_NGSAtlas contains 43 DNA methylation profiles and 37 transcription profiles detected by MeDIP-Seq and RNA-Seq, respectively, in two distinct brain regions and peripheral blood of SZ, BP and non-psychiatric controls. In addition to these data that were generated in-house, we have included, and will continue to include, published DNA methylation and gene expression data from other research groups, with a focus on psychiatric disorders. A flexible query engine has been developed for the acquisition of methylation profiles and transcription profiles for special genes or genomic regions of interest of the selected samples. Furthermore, the PD_NGSAtlas offers online tools for identifying aberrantly methylated and expressed events involved in psychiatric disorders. A genome browser has been developed to provide integrative and detailed views of multidimensional data in a given genomic context, which can help researchers understand molecular mechanisms from epigenetic and transcriptional perspectives. Moreover, users can download the methylation and transcription data for further analyses.ConclusionsThe PD_NGSAtlas aims to provide storage of epigenomic and transcriptomic data as well as quantitative analyses of epigenetic and transcriptional alterations involved in psychiatric disorders. The PD_NGSAtlas will be a valuable data resource and will enable researchers to investigate the pathophysiology and aetiology of disease in detail. The database is available at http://bioinfo.hrbmu.edu.cn/pd_ngsatlas/.

Dataset Information

Genomic, transcriptomic and epigenomic sequencing data of the B-cell leukemia cell line REH.

Objectives

Data description

Publications

Genomic, transcriptomic and epigenomic sequencing data of the B-cell leukemia cell line REH.

Similar Datasets

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