BLUEPRINT ATAC-seq data for cells in the haematopoietic lineages, from adult and cord blood samples

BLLUEPRINT ATAC-seq data for cells in the haematopoietic lineages, from adult and cord blood samples.

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

29 Datasets 2 Publications

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
EGAD00001002693	Innate immune memory is the phenomenon whereby innate immune cells such as monocytes or macrophages undergo functional reprogramming after exposure to microbial components such as LPS. We apply an integrated epigenomic approach to characterize the molecular events involved in LPS-induced tolerance in a time dependent manner. ChIP-seq, RNA-seq, WGBS and ATAC-seq data were generated. This analysis identified epigenetic programs in tolerance and trained macrophages, and the potential transcription factors involved. Experimental set-up Time-course in vitro culture of human monocytes. Two innate immune memory states can be induced in culture through an initial exposure of primary human monocytes to either LPS or BG for 24 hours, followed by removal of stimulus and differentiation to macrophages for an additional 5 days. Cells were collected at baseline (day 0), 1 hour, 4 hour, 24 hour and 6 days.	Illumina HiSeq 2000 NextSeq 500 unspecified	71
EGAD00001002708	ATAC-seq data for 7 sample(s) from tonsil, on Genome GRCh38. 7 run(s), 7 experiment(s), 7 alignment(s). Part of BLUEPRINT (September 2016).	NextSeq 500	7
EGAD00001002709	ATAC-seq data for 136 sample(s) from venous blood, on Genome GRCh38. 141 run(s), 139 experiment(s), 139 alignment(s). Part of BLUEPRINT (September 2016).	NextSeq 500	136
EGAD00001002710	ATAC-seq data for 4 sample(s) from bone marrow, on Genome GRCh38. 4 run(s), 4 experiment(s), 4 alignment(s). Part of BLUEPRINT (September 2016).	NextSeq 500	4
EGAD00001002899	ATAC-seq data for 1 sample(s) for monocyte RPMI_T=4hrs from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016).	NextSeq 500	1
EGAD00001002900	ATAC-seq data for 1 sample(s) for monocyte RPMI_LPS_T=24hrs from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016).	NextSeq 500	1
EGAD00001002901	ATAC-seq data for 2 sample(s) for monocyte RPMI_LPS_T=24hrs_RPMI_T=5days from venous blood, on Genome GRCh38. 2 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT (September 2016).	NextSeq 500	2
EGAD00001002902	ATAC-seq data for 3 sample(s) for naive B cell from venous blood, on Genome GRCh38. 3 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT (September 2016).	NextSeq 500	3
EGAD00001002903	ATAC-seq data for 3 sample(s) for naive B cell from tonsil, on Genome GRCh38. 3 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT (September 2016).	NextSeq 500	3
EGAD00001002904	ATAC-seq data for 1 sample(s) for monocyte RPMI_BG_T=24hrs_RPMI_T=5days from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016).	NextSeq 500	1
EGAD00001002905	ATAC-seq data for 3 sample(s) for unswitched memory B cell from venous blood, on Genome GRCh38. 3 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT (September 2016).	NextSeq 500	3
EGAD00001002906	ATAC-seq data for 1 sample(s) for monocyte RPMI_BG_T=1hr from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016).	NextSeq 500	1
EGAD00001002907	ATAC-seq data for 2 sample(s) for osteoclast from venous blood, on Genome GRCh38. 2 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT (September 2016).	NextSeq 500	2
EGAD00001002908	ATAC-seq data for 2 sample(s) for class switched memory B cell from venous blood, on Genome GRCh38. 2 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT (September 2016).	NextSeq 500	2
EGAD00001002909	ATAC-seq data for 1 sample(s) for monocyte RPMI_BG_T=24hrs from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016).	NextSeq 500	1
EGAD00001002910	ATAC-seq data for 1 sample(s) for monocyte RPMI_BG_T=4hrs from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016).	NextSeq 500	1
EGAD00001002911	ATAC-seq data for 1 sample(s) for germinal center B cell from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016).	NextSeq 500	1
EGAD00001002912	ATAC-seq data for 2 sample(s) for plasma cell from tonsil, on Genome GRCh38. 2 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT (September 2016).	NextSeq 500	2
EGAD00001002913	ATAC-seq data for 1 sample(s) for monocyte RPMI_LPS_T=1hr from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016).	NextSeq 500	1
EGAD00001002914	ATAC-seq data for 1 sample(s) for monocyte RPMI_T=6days from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016).	NextSeq 500	1
EGAD00001002915	ATAC-seq data for 1 sample(s) for monocyte RPMI_BG_T=24hrs_RPMI_T=5days_LPS_T=4hrs from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016).	NextSeq 500	1
EGAD00001002916	ATAC-seq data for 106 sample(s) Chronic Lymphocytic Leukemia from venous blood, on Genome GRCh38. 111 run(s), 109 experiment(s), 109 alignment(s). Part of BLUEPRINT (September 2016).	NextSeq 500	106
EGAD00001002917	ATAC-seq data for 2 sample(s) for germinal center B cell from tonsil, on Genome GRCh38. 2 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT (September 2016).	NextSeq 500	2
EGAD00001002918	ATAC-seq data for 5 sample(s) Mantle Cell Lymphoma from venous blood, on Genome GRCh38. 5 run(s), 5 experiment(s), 5 alignment(s). Part of BLUEPRINT (September 2016).	NextSeq 500	5
EGAD00001002919	ATAC-seq data for 1 sample(s) for monocyte RPMI_T=1hr from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016).	NextSeq 500	1
EGAD00001002920	ATAC-seq data for 4 sample(s) Multiple Myeloma for plasma cell from bone marrow, on Genome GRCh38. 4 run(s), 4 experiment(s), 4 alignment(s). Part of BLUEPRINT (September 2016).	NextSeq 500	4
EGAD00001002921	ATAC-seq data for 1 sample(s) for monocyte RPMI_T=24hrs from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016).	NextSeq 500	1
EGAD00001002922	ATAC-seq data for 1 sample(s) for monocyte RPMI_LPS_T=4hrs from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016).	NextSeq 500	1
EGAD00001004046	Analysis of the reference epigenomes and regulatory landscape of CLL as a whole and its major clinico-biological subtypes (with mutated and unmutated IGHV) in the light of the normal B-cell differentiation. We have extensively characterized the reference epigenomes of seven primary chronic lymphocytic leukemia samples (CLLs) with mutated (n=5) and unmutated IGHV (n=2) as well as several mature B-cell subpopulations (naive B cells from blood and tonsil, germinal center B cells, memory B cells and plasma cells from tonsil) using genome-wide maps of six histone marks (H3K4me3, H3K4me1, H3K27ac, H3K36me3, H3K9me3 and H3K27me3), DNA accessibility (ATAC-seq), DNA methylation (whole-genome bisulfite sequencing) and gene expression (RNA-seq). Furthermore, we have mapped the regulatory chromatin landscape of 100 additional CLL cases using chIP-seq of H3K27ac and ATAC-seq and linked these data to additional layers of information (whole-genome and/or whole-exome sequencing (WGS/WES), RNA-seq and DNA methylation microarrays) studied in the context of the International Cancer Genome Consortium (ICGC).	Illumina HiSeq 2000 NextSeq 500	303

Publications	Citations
Chromatin activation as a unifying principle underlying pathogenic mechanisms in multiple myeloma. Ordoñez R, Kulis M, Russiñol N, Chapaprieta V, Carrasco-Leon A, García-Torre B, Charalampopoulou S, Clot G, Beekman R, Meydan C, Duran-Ferrer M, Verdaguer-Dot N, Vilarrasa-Blasi R, Soler-Vila P, Garate L, Miranda E, San José-Enériz E, Rodriguez-Madoz JR, Ezponda T, Martínez-Turrilas R, Vilas-Zornoza A, Lara-Astiaso D, Dupéré-Richer D, Martens JHA, El-Omri H, Taha RY, Calasanz MJ, Paiva B, San Miguel J, Flicek P, Gut I, Melnick A, Mitsiades CS, Licht JD, Campo E, Stunnenberg HG, Agirre X, Prosper F, Martin-Subero JI. Genome Res 30: 2020 1217-1227	29
Dynamics of genome architecture and chromatin function during human B cell differentiation and neoplastic transformation. Vilarrasa-Blasi R, Soler-Vila P, Verdaguer-Dot N, Russiñol N, Di Stefano M, Chapaprieta V, Clot G, Farabella I, Cuscó P, Kulis M, Agirre X, Prosper F, Beekman R, Beà S, Colomer D, Stunnenberg HG, Gut I, Campo E, Marti-Renom MA, Martin-Subero JI. Nat Commun 12: 2021 651	55

Publications

Citations

Chromatin activation as a unifying principle underlying pathogenic mechanisms in multiple myeloma.
Ordoñez R, Kulis M, Russiñol N, Chapaprieta V, Carrasco-Leon A, García-Torre B, Charalampopoulou S, Clot G, Beekman R, Meydan C, Duran-Ferrer M, Verdaguer-Dot N, Vilarrasa-Blasi R, Soler-Vila P, Garate L, Miranda E, San José-Enériz E, Rodriguez-Madoz JR, Ezponda T, Martínez-Turrilas R, Vilas-Zornoza A, Lara-Astiaso D, Dupéré-Richer D, Martens JHA, El-Omri H, Taha RY, Calasanz MJ, Paiva B, San Miguel J, Flicek P, Gut I, Melnick A, Mitsiades CS, Licht JD, Campo E, Stunnenberg HG, Agirre X, Prosper F, Martin-Subero JI. Genome Res 30: 2020 1217-1227

Dynamics of genome architecture and chromatin function during human B cell differentiation and neoplastic transformation.
Vilarrasa-Blasi R, Soler-Vila P, Verdaguer-Dot N, Russiñol N, Di Stefano M, Chapaprieta V, Clot G, Farabella I, Cuscó P, Kulis M, Agirre X, Prosper F, Beekman R, Beà S, Colomer D, Stunnenberg HG, Gut I, Campo E, Marti-Renom MA, Martin-Subero JI. Nat Commun 12: 2021 651