ATAC-seq count data from primary pediatric AML samples

ATAC-seq Data from Primary Pediatric AML Samples

Data Source

Primary pediatric AML patient ATAC-seq data were obtained from Yokohama City University (YCU) and published in:

Yamato G, Kawai T, Shiba N, Ikeda J, Hara Y, Ohki K, Tsujimoto S. I., Kaburagi T, Yoshida K, Shiraishi Y, Miyano S, Kiyokawa N, Tomizawa D, Shimada A, Sotomatsu M, Arakawa H, Adachi S, Taga T, Horibe K, Ogawa S, Hata K, Hayashi Y. Genome-wide DNA methylation analysis in pediatric acute myeloid leukemia. Blood Adv. 2022 Jun 14;6(11):3207-3219. doi: 10.1182/bloodadvances.2021005381. PMID: 35008106; PMCID: PMC9198913.

Bioinformatic Processing

A modified version of the ATAC-seq Data Processing Pipeline (Reichl, S. et al. Ultimate ATAC-seq Data Processing & Quantification Pipeline. (2024)) was applied to the raw BAM files, accessible at: https://github.com/epigen/atacseq_pipeline.

The pipeline utilized fastp (Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884–i890 (2018)) for adapter removal and Bowtie2 (Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012)) for read alignment to the GRCh38 (hg38) human reference genome.

Duplicate marking was performed with samblaster (Faust, G. G. & Hall, I. M. SAMBLASTER: fast duplicate marking and structural variant read extraction. Bioinformatics 30, 2503–2505 (2014)). The aligned BAM files were sorted, indexed, and filtered for ENCODE blacklisted regions using samtools (Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009)).

Counts over exons were obtained using featureCounts (Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general-purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923–930 (2014)).

Data Structure

The table contains the following columns:

Column Name
Description

NCBI_id
RefSeq (NCBI Reference Sequence) accession number for a specific mRNA transcript

Gene_symbol
Official gene symbol

ENTREZ_id
Entrez Gene ID

YCU_NUP98-NSD1+PRDM16high-AM
Read counts per gene for this sample

YCU_NUP98-NSD1+PRDM16high-HR
Read counts per gene for this sample

YCU_RUNX1-RUNX1T1-SR
Read counts per gene for this sample

YCU_t11-19MLL_KA
Read counts per gene for this sample

YCU_t11-19MLL-NR
Read counts per gene for this sample