Epigenetic profiling of acute myeloid leukemia - EGA European Genome-phenome Archive

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00010002775	This dataset includes IDAT files from 424 AML samples. The samples were profiled using the Illumina Infinium Methylation EPIC array.	Illumina Infinium Methylation EPIC array	424
EGAD50000001426	Bulk ATAC-seq was performed for 1563 AML cases. Library was constructed using the Fast-ATAC protocol as previously described. The resulting library was sequenced using NovaSeq 6000 instrument (Illumina) with a paired-end protocol. Two paired fastq files were stored.	Illumina NovaSeq 6000	1558
EGAD50000001427	ChIP-seq was performed in 234 AML cases with input controls. The antibodies used for ChIP were as follows: SMC1 (Abcam, ab9262), CTCF (Cell Signaling Technology, D31H2), RPB1 (CST, D8L4Y), H3K27ac (Cell Signaling Technology, D5E4), and H3K27me3 (Cell Signaling Technology, C36B11). The resulting library was sequenced using NovaSeq 6000 instrument (Illumina) with a paired-end protocol. Two paired fastq files were stored.	Illumina NovaSeq 6000	240
EGAD50000001428	Single-cell matched RNA-seq and ATAC-seq experiments were performed in 4 AML remission samples using the Next GEM Single Cell Multiome ATAC + Gene Expression. The scATAC libraries were sequenced using DNBSEQ G400 (MGI) instrument with a custom protocol (Read 1: 50 cycles, Read 2: 49 cycles, i5 Index: 24 cycles, i7 Index: 8 cycles). The scRNA libraries were sequenced using DNBSEQ G400 (MGI) instrument with a custom protocol (Read 1: 28 cycles, Read 2: 90 cycles). Cell Ranger ARC (10x Genomics) was used for data processing to generate bam files and count matrices for scRNA and scATAC with the hg19 reference genome and GENCODE human v19 annotation. The bam files for scRNA and scATAC were stored.	DNBSEQ-G400	4
EGAD50000001429	Bulk ATAC-seq was performed for 11 AML cell lines. Library was constructed using the Fast-ATAC protocol as previously described. The resulting library was sequenced using NovaSeq 6000 instrument (Illumina) with a paired-end protocol. Two paired fastq files were stored.	Illumina NovaSeq 6000	11
EGAD50000001430	Bulk ATAC-seq was performed for 25 normal bone marrow cells, with or without mononuclear cell purificatrion. Library was constructed using the Fast-ATAC protocol as previously described. The resulting library was sequenced using NovaSeq 6000 instrument (Illumina) with a paired-end protocol. Two paired fastq files were stored.	Illumina NovaSeq 6000	50
EGAD50000001431	Single-cell matched RNA-seq and ATAC-seq experiments were performed in 36 AML cases using the Next GEM Single Cell Multiome ATAC + Gene Expression. The scATAC libraries were sequenced using DNBSEQ G400 (MGI) instrument with a custom protocol (Read 1: 50 cycles, Read 2: 49 cycles, i5 Index: 24 cycles, i7 Index: 8 cycles). The scRNA libraries were sequenced using DNBSEQ G400 (MGI) instrument with a custom protocol (Read 1: 28 cycles, Read 2: 90 cycles). Cell Ranger ARC (10x Genomics) was used for data processing to generate bam files and count matrices for scRNA and scATAC with the hg19 reference genome and GENCODE human v19 annotation. The bam files for scRNA and scATAC were stored.	DNBSEQ-G400	35
EGAD50000001432	Bulk RNA-seq was performed for 1,398 AML cases. Libraries for RNA-seq were prepared using the NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina (New England BioLabs). The generated libraries were subjected to sequencing using NovaSeq 6000 instrument (Illumina) with a paired-end protocol. Two paired fastq files were stored.	Illumina NovaSeq 6000	1394

Publications	Citations
Chromatin landscape and epigenetic heterogeneity of acute myeloid leukaemia. Ochi Y, Liew-Littorin M, Nannya Y, Bengtzen S, Piauger B, Deneberg S, Jädersten M, Lazarevic V, Cammenga J, Robelius A, Wennström L, Ölander E, Kasahara S, Hiramoto N, Kanemura N, Sezaki N, Sakurada M, Iwasaki M, Kanda J, Ueda Y, Yoshihara S, Erkers T, Struyf N, Watanabe Y, Motomura M, Nakagawa MM, Saiki R, Fukushima H, Okazaki K, Morimoto S, Yoda A, Okuda R, Komatsu S, Xie G, Österroos A, Kon A, Zhao L, Shiraishi Y, Ishikawa T, Miyano S, Katayama K, Imoto S, Matsuda S, Takaori-Kondo A, Aburatani H, Suzuki HI, Kallioniemi O, Juliusson G, Höglund M, Lehmann S, Ogawa S. Nature 656: 2026 752-762	1

Publications

Citations

Chromatin landscape and epigenetic heterogeneity of acute myeloid leukaemia.
Ochi Y, Liew-Littorin M, Nannya Y, Bengtzen S, Piauger B, Deneberg S, Jädersten M, Lazarevic V, Cammenga J, Robelius A, Wennström L, Ölander E, Kasahara S, Hiramoto N, Kanemura N, Sezaki N, Sakurada M, Iwasaki M, Kanda J, Ueda Y, Yoshihara S, Erkers T, Struyf N, Watanabe Y, Motomura M, Nakagawa MM, Saiki R, Fukushima H, Okazaki K, Morimoto S, Yoda A, Okuda R, Komatsu S, Xie G, Österroos A, Kon A, Zhao L, Shiraishi Y, Ishikawa T, Miyano S, Katayama K, Imoto S, Matsuda S, Takaori-Kondo A, Aburatani H, Suzuki HI, Kallioniemi O, Juliusson G, Höglund M, Lehmann S, Ogawa S. Nature 656: 2026 752-762