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Series GSE159608 Query DataSets for GSE159608
Status Public on Jun 10, 2021
Title Automated CUT&Tag profiling of chromatin heterogeneity in mixed-lineage leukemia
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Acute myeloid and lymphoid leukemias often harbor chromosomal translocations involving the Mixed Lineage Leukemia-1 gene, which encodes the KMT2A lysine methyltransferase. The most common translocations produce in-frame fusions of KMT2A to trans-activation domains of chromatin regulatory proteins. Here we develop a strategy to map the genome-wide occupancy of oncogenic KMT2A fusion proteins in primary patient samples regardless of fusion partner. By modifying the versatile CUT&Tag method for full automation we identify common and tumor-specific patterns of aberrant chromatin regulation induced by different KMT2A fusion proteins. Integration of automated and single-cell CUT&Tag uncovers lineage heterogeneity within patient samples and provides an attractive avenue for future diagnostics.
Overall design We used Cleavage under targets and Tagmentation (Cut-and-Tag), a chromatin profiling strategy in which antibody-targeted controlled integration of DNA sequencing adapters produces libraries for paired-end DNA sequencing.
Contributor(s) Janssens DH, Meers MP, Wu SJ, Babaeva E, Meshinchi S, Sarthy JF, Ahmad K, Henikoff S
Citation(s) 34663924
NIH grant(s)
Grant ID Grant title Affiliation Name
R01 HG010492 Epigenomic profiling of complex tissues with single-cell CUT&RUN FRED HUTCHINSON CANCER RESEARCH CENTER Steven Henikoff
F32 GM129954 Analyzing pioneer factor dynamics and function during differentiation and reprogramming FRED HUTCHINSON CANCER RESEARCH CENTER Michael P Meers
Submission date Oct 19, 2020
Last update date Dec 16, 2021
Contact name Jorja Henikoff
Phone 206-667-4850
Organization name Fred Hutchinson Cancer Research Center
Department Basic Sciences
Lab Henikoff
Street address 1100 Fairview AV N, A1-162
City Seattle
State/province WA
ZIP/Postal code 98109-1024
Country USA
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (419)
GSM4835651 ALL1_Dot1L_AutoCUTnTag_(20200528_DJ_Hs_Dot1_TB13_0520)
GSM4835652 ALL1_ELL_AutoCUTnTag_(20200528_DJ_Hs_ELL_TB13_0520)
GSM4835653 ALL1_ENL_AutoCUTnTag_(20200528_DJ_Hs_ENL_TB13_0520)
BioProject PRJNA669859
SRA SRP287674

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE159608_AutoCUTnRUN_protocols_io.pdf 6.1 Mb (ftp)(http) PDF
GSE159608_AutoCUTnTag_protocols_io.pdf 5.3 Mb (ftp)(http) PDF 2.7 Mb (ftp)(http) PDF
GSE159608_CnTathome_Protocols_io.pdf 1.6 Mb (ftp)(http) PDF
GSE159608_RAW.tar 17.5 Gb (http)(custom) TAR (of BED, BEDGRAPH, TSV)
GSE159608_iCell8_scCnT_protocol.pdf 35.4 Kb (ftp)(http) PDF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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