Data sources
Public ATACseq, ChIPseq, and RNAseq datasets were downloaded from the Gene Expression Omnibus, Array Express, https://biodev.github.io/BeatAML2/ and https://depmap.org/portal/download/all/?releasename=DepMap+Public+23Q2&filename=OmicsExpressionGenesExpectedCountProfile.csv Data sources are detailed in Table 1.
ATACseq
Sequencing reads were aligned to the hg38 reference genome using BWA (1), duplicate and mitochondrial reads removed, and peak calling was performed using MACS2 (2). deepTools bamCoverage (3) was used to produce RPKM-normalised genome coverage profiles for visualisation on the UCSC genome browser.
ChIPseq/ChIPmentation
Sequencing reads were aligned to the hg38 reference genome using BWA (1) and peak calling was performed using MACS2 (2). deepTools bamCoverage (3) was used to produce RPKM-normalised genome coverage profiles for visualisation on the UCSC genome browser.
RNAseq
Processed count tables were downloaded (Table 1) and normalised. Expression plots were created using plotly.
References
- Li, H. and Durbin, R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760.
- Zhang, Y., Liu, T., Meyer, C.A., Eeckhoute, J., Johnson, D.S., Bernstein, B.E., Nusbaum, C., Myers, R.M., Brown, M., Li, W. et al. (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol, 9, R137.
- Ramirez, F., Dundar, F., Diehl, S., Gruning, B.A. and Manke, T. (2014) deepTools: a flexible platform for exploring deep-sequencing data. Nucleic Acids Res, 42, W187-191.
How to cite
Julie A I Thoms, Forrest C Koch, Alireza Raei, Shruthi Subramanian, Jason W H Wong, Fatemeh Vafaee, John E Pimanda (2023) BloodChIP Xtra: an expanded database of comparative genome-wide transcription factor binding and gene-expression profiles in healthy human stem/progenitor subsets and leukemic cells. Nucleic Acids Research, https://doi.org/10.1093/nar/gkad918
Table 1:
|
Cell_type |
Factor |
PMID |
Accession |
SRA identifier |
|---|---|---|---|---|
|
Kasumi-1 |
ATAC |
34010414 |
E-MTAB-9021 |
ERR4084850_ERR4084851_ERR4084852 (Array Express) |
|
Kasumi-1 |
ERG |
27851970 |
GSM2026052 |
|
|
Kasumi-1 |
FLI1 |
27851970 |
GSM2026051 |
|
|
Kasumi-1 |
GATA2 |
27851970 |
GSM2026054 |
|
|
Kasumi-1 |
H3K27Ac |
36215477 |
GSM6282797 |
|
|
Kasumi-1 |
LMO2 |
23812588 |
GSM1082311 |
|
|
Kasumi-1 |
LYL1 |
27851970 |
GSM2026056 |
|
|
Kasumi-1 |
PU.1 |
25242324 |
GSM1501166 |
|
|
Kasumi-1 |
RUNX1 |
27851970 |
GSM2026066 |
|
|
Kasumi-1 |
TAL1 |
27851970 |
GSM2026055 |
|
|
KG-1 |
ATAC |
35015684 |
GSE167869 |
SRR13800827_SRR13800828 |
|
KG-1 |
ERG |
34075404 |
GSM4810544 |
|
|
KG-1 |
FLI1 |
34075404 |
GSM4810545 |
|
|
KG-1 |
GATA2 |
34075404 |
GSM4810546 |
|
|
KG-1 |
H3K27Ac |
34075404 |
GSM4810547 |
|
|
KG-1 |
LMO2 |
34075404 |
GSM4810549 |
|
|
KG-1 |
LYL1 |
34075404 |
GSM4810550 |
|
|
KG-1 |
PU.1 |
31964861 |
GSM3686961 |
|
|
KG-1 |
RUNX1 |
34075404 |
GSM4810551 |
|
|
KG-1 |
TAL1 |
34075404 |
GSM4810552 |
|
|
ME-1 |
ATAC |
29958106 |
GSE101790 |
SRR5861512_SRR5861513 |
|
ME-1 |
ERG |
24002588 |
GSM1122314 |
SRR826876 |
|
ME-1 |
FLI1 |
24002588 |
GSM1122312 |
SRR826874 |
|
ME-1 |
GATA2 |
24002588 |
GSM1122310 |
SRR826872 |
|
ME-1 |
H3K27Ac |
34075404 |
GSM4810554 |
|
|
ME-1 |
LMO2 |
34075404 |
GSM4810556 |
|
|
ME-1 |
LYL1 |
34075404 |
GSM4810557 |
|
|
ME-1 |
PU.1 |
24002588 |
GSM1122315 |
SRR826877 |
|
ME-1 |
RUNX1 |
24002588 |
GSM1122306 |
SRR826868 |
|
ME-1 |
TAL1 |
24002588 |
GSM1122311 |
SRR826873 |
|
TSU-1621-MT |
ERG |
26148230 |
GSM1480735 |
|
|
TSU-1621-MT |
FLI1 |
26148230 |
GSM1480740 |
|
|
TSU-1621-MT |
GATA2 |
26148230 |
GSM1480746 |
|
|
TSU-1621-MT |
LMO2 |
26148230 |
GSM1480745 |
|
|
TSU-1621-MT |
LYL1 |
26148230 |
GSM1480747 |
|
|
TSU-1621-MT |
PU.1 |
26148230 |
GSM1557623 |
|
|
TSU-1621-MT |
RUNX1 |
26148230 |
GSM1480744 |
|
|
TSU-1621-MT |
TAL1 |
26148230 |
GSM1480748 |
|
|
Bulk CD34+ HSPC |
IgG |
23974199 |
GSM1097886 |
SRR772113 |
|
Composite IgG |
IgG |
37595278 |
GSE231486 |
SRR24388652_SRR24388695_SRR24388748_SRR24388793 |
|
KG-1 |
IgG |
34075404 |
GSM4810548 |
|
|
ME-1 |
IgG |
34075404 |
GSM4810555 |
|
|
CMP |
ATAC |
27526324 |
GSE74912 |
SRR2920469_ SRR2920470_ SRR2920481_ SRR2920482_ SRR2920500_ SRR2920501_ SRR2920536_ SRR2920537 |
|
CMP |
CTCF |
37595278 |
GSE231486 |
SRR24388763_SRR24388764_SRR24388765 |
|
CMP |
ERG |
37595278 |
GSE231486 |
SRR24388800_SRR24388801_SRR24388802 |
|
CMP |
FLI1 |
37595278 |
GSE231486 |
SRR24388797_SRR24388798_SRR24388799 |
|
CMP |
GATA2 |
37595278 |
GSE231486 |
SRR24388794_SRR24388795_SRR24388796 |
|
CMP |
H3K27ac |
37595278 |
GSE231486 |
SRR24385755_SRR24386298_SRR24386299 |
|
CMP |
H3K27ac HiChIP |
37595278 |
GSE231486 |
SRR24386298_SRR24386299 |
|
CMP |
H3K27me3 |
37595278 |
GSE231486 |
SRR24388673 |
|
CMP |
H3K4me3 |
37595278 |
GSE231486 |
SRR24385750 |
|
CMP |
LMO2 |
37595278 |
GSE231486 |
SRR24388790_SRR24388791_SRR24388792 |
|
CMP |
LYL1 |
37595278 |
GSE231486 |
SRR24388787_SRR24388788_SRR24388789 |
|
CMP |
POL2 |
37595278 |
GSE231486 |
SRR24388680_SRR24388722 |
|
CMP |
PU.1 |
37595278 |
GSE231486 |
SRR24388729_SRR24388730_SRR24388731 |
|
CMP |
RUNX1 |
37595278 |
GSE231486 |
SRR24388784_SRR24388785_SRR24388786 |
|
CMP |
STAG2 |
37595278 |
GSE231486 |
SRR24388716_SRR24388724 |
|
CMP |
TAL1 |
37595278 |
GSE231486 |
SRR24388781_SRR24388782_SRR24388783 |
|
GMP |
ATAC |
27526324 |
GSE74912 |
SRR2920471_ SRR2920472_ SRR2920483_ SRR2920484_ SRR2920538_ SRR2920539 |
|
GMP |
CTCF |
37595278 |
GSE231486 |
SRR24388759_SRR24388760_SRR24388761_SRR24388762 |
|
GMP |
ERG |
37595278 |
GSE231486 |
SRR24388704_SRR24388705_SRR24388706_SRR24388707 |
|
GMP |
FLI1 |
37595278 |
GSE231486 |
SRR24388700_SRR24388701_SRR24388702_SRR24388703 |
|
GMP |
GATA2 |
37595278 |
GSE231486 |
SRR24388696_SRR24388697_SRR24388698_SRR24388699 |
|
GMP |
H3K27ac |
37595278 |
GSE231486 |
SRR24385754_SRR24386292_SRR24386293 |
|
GMP |
H3K27ac HiChIP |
37595278 |
GSE231486 |
SRR24386292_SRR24386293 |
|
GMP |
H3K27me3 |
37595278 |
GSE231486 |
SRR24388672 |
|
GMP |
H3K4me3 |
37595278 |
GSE231486 |
SRR24385749 |
|
GMP |
LMO2 |
37595278 |
GSE231486 |
SRR24388691_SRR24388692_SRR24388693_SRR24388694 |
|
GMP |
LYL1 |
37595278 |
GSE231486 |
SRR24388687_SRR24388688_SRR24388689_SRR24388690 |
|
GMP |
POL2 |
37595278 |
GSE231486 |
SRR24388678_SRR24388679 |
|
GMP |
PU.1 |
37595278 |
GSE231486 |
SRR24388725_SRR24388726_SRR24388727_SRR24388728 |
|
GMP |
RUNX1 |
37595278 |
GSE231486 |
SRR24388669_SRR24388670_SRR24388685_SRR24388686 |
|
GMP |
STAG2 |
37595278 |
GSE231486 |
SRR24388708_SRR24388709_SRR24388713_SRR24388714 |
|
GMP |
TAL1 |
37595278 |
GSE231486 |
SRR24388665_SRR24388666_SRR24388667_SRR24388668 |
|
HSC-MPP |
ATAC |
27526324 |
GSE74912 |
SRR2920466_ SRR2920477_ SRR2920478_ SRR2920506_ SRR2920507_ SRR2920531_ SRR2920532 |
|
HSC-MPP |
CTCF |
37595278 |
GSE231486 |
SRR24388766_SRR24388767_SRR24388768 |
|
HSC-MPP |
ERG |
37595278 |
GSE231486 |
SRR24388755_SRR24388756_SRR24388780 |
|
HSC-MPP |
FLI1 |
37595278 |
GSE231486 |
SRR24388752_SRR24388753_SRR24388754 |
|
HSC-MPP |
GATA2 |
37595278 |
GSE231486 |
SRR24388749_SRR24388750_SRR24388751 |
|
HSC-MPP |
H3K27ac |
37595278 |
GSE231486 |
SRR24385756_SRR24386294_SRR24386295_SRR24386296_SRR24386297 |
|
HSC-MPP |
H3K27ac HiChIP |
37595278 |
GSE231486 |
SRR24386294_SRR24386295_SRR24386296_SRR24386297 |
|
HSC-MPP |
H3K27me3 |
37595278 |
GSE231486 |
SRR24388674 |
|
HSC-MPP |
H3K4me3 |
37595278 |
GSE231486 |
SRR24385751 |
|
HSC-MPP |
LMO2 |
37595278 |
GSE231486 |
SRR24388745_SRR24388746_SRR24388747 |
|
HSC-MPP |
LYL1 |
37595278 |
GSE231486 |
SRR24388742_SRR24388743_SRR24388744 |
|
HSC-MPP |
POL2 |
37595278 |
GSE231486 |
SRR24388681_SRR24388682 |
|
HSC-MPP |
PU.1 |
37595278 |
GSE231486 |
SRR24388732_SRR24388733_SRR24388734 |
|
HSC-MPP |
RUNX1 |
37595278 |
GSE231486 |
SRR24388739_SRR24388740_SRR24388741 |
|
HSC-MPP |
STAG2 |
37595278 |
GSE231486 |
SRR24388717_SRR24388718 |
|
HSC-MPP |
TAL1 |
37595278 |
GSE231486 |
SRR24388712_SRR24388737_SRR24388738 |
|
HSC-MPP |
ATAC |
27526324 |
GSE74912 |
SRR2920466_ SRR2920477_ SRR2920478_ SRR2920506_ SRR2920507_ SRR2920531_ SRR2920532_ SRR2920467_ SRR2920479_ SRR2920509_ SRR2920510_ SRR2920533_ SRR2920534 |
|
MEP |
ATAC |
27526324 |
GSE74912 |
SRR2920473_ SRR2920474_ SRR2920485_ SRR2920486_ SRR2920508_ SRR2920540_ SRR2920541 |
|
MEP |
CTCF |
37595278 |
GSE231486 |
SRR24388735_SRR24388736_SRR24388757_SRR24388758 |
|
MEP |
ERG |
37595278 |
GSE231486 |
SRR24388661_SRR24388662_SRR24388663_SRR24388664 |
|
MEP |
FLI1 |
37595278 |
GSE231486 |
SRR24388657_SRR24388658_SRR24388659_SRR24388660 |
|
MEP |
GATA2 |
37595278 |
GSE231486 |
SRR24388653_SRR24388654_SRR24388655_SRR24388656 |
|
MEP |
H3K27ac |
37595278 |
GSE231486 |
SRR24385753_SRR24386290_SRR24386291 |
|
MEP |
H3K27ac HiChIP |
37595278 |
GSE231486 |
SRR24386290_SRR24386291 |
|
MEP |
H3K27me3 |
37595278 |
GSE231486 |
SRR24388671 |
|
MEP |
H3K4me3 |
37595278 |
GSE231486 |
SRR24385752 |
|
MEP |
LMO2 |
37595278 |
GSE231486 |
SRR24388648_SRR24388649_SRR24388650_SRR24388651 |
|
MEP |
LYL1 |
37595278 |
GSE231486 |
SRR24388647_SRR24388777_SRR24388778_SRR24388779 |
|
MEP |
POL2 |
37595278 |
GSE231486 |
SRR24388675_SRR24388676_SRR24388677_SRR24388715 |
|
MEP |
PU.1 |
37595278 |
GSE231486 |
SRR24388719_SRR24388720_SRR24388721_SRR24388723 |
|
MEP |
RUNX1 |
37595278 |
GSE231486 |
SRR24388773_SRR24388774_SRR24388775_SRR24388776 |
|
MEP |
STAG2 |
37595278 |
GSE231486 |
SRR24388683_SRR24388684_SRR24388710_SRR24388711 |
|
MEP |
TAL1 |
37595278 |
GSE231486 |
SRR24388769_SRR24388770_SRR24388771_SRR24388772 |
|
MPP |
ATAC |
27526324 |
GSE74912 |
SRR2920467_ SRR2920479_ SRR2920509_ SRR2920510_ SRR2920533_ SRR2920534 |
|
SU209_Blast |
ATAC |
27526324 |
GSM1937468 |
SRR2920558 |
|
SU353_Blast |
ATAC |
27526324 |
GSM1937479 |
SRR2920569 |
|
SU444_Blast |
ATAC |
27526324 |
GSM1937482 |
SRR2920572 |
|
SU496_Blast |
ATAC |
27526324 |
GSM1937487 |
SRR2920577 |
|
SU575_Blast |
ATAC |
27526324 |
GSM1937492 |
SRR2920582 |
|
SU583_Blast |
ATAC |
27526324 |
GSM1937495 |
SRR2920585 |
|
SU654_Blast |
ATAC |
27526324 |
GSM1937503 |
SRR2920593 |
|
SU070_Blast |
ATAC |
27526324 |
GSE74912 |
SRR2920553_SRR2920554 |
|
SU209_LSC |
ATAC |
27526324 |
GSM1937469 |
SRR2920559 |
|
SU353_LSC |
ATAC |
27526324 |
GSM1937480 |
SRR2920570 |
|
SU444_LSC |
ATAC |
27526324 |
GSM1937483 |
SRR2920573 |
|
SU496_LSC |
ATAC |
27526324 |
GSM1937488 |
SRR2920578 |
|
SU575_LSC |
ATAC |
27526324 |
GSM1937493 |
SRR2920583 |
|
SU583_LSC |
ATAC |
27526324 |
GSM1937496 |
SRR2920586 |
|
SU654_LSC |
ATAC |
27526324 |
GSM1937504 |
SRR2920594 |
|
SU070_LSC |
ATAC |
27526324 |
GSM1937465 |
SRR2920555 |
|
SU209_pHSC |
ATAC |
27526324 |
GSE74912 |
SRR2920560_SRR2920562_SRR2920561 |
|
SU353_pHSC |
ATAC |
27526324 |
GSM1937481 |
SRR2920571 |
|
SU444_pHSC |
ATAC |
27526324 |
GSM1937484 |
SRR2920574 |
|
SU496_pHSC |
ATAC |
27526324 |
GSM1937489 |
SRR2920579 |
|
SU575_pHSC |
ATAC |
27526324 |
GSM1937494 |
SRR2920584 |
|
SU583_pHSC |
ATAC |
27526324 |
GSE74912 |
SRR2920587_SRR2920588 |
|
SU654_pHSC |
ATAC |
27526324 |
GSM1937505 |
SRR2920595 |
|
SU070_pHSC |
ATAC |
27526324 |
GSE74912 |
SRR2920556_SRR2920557 |
|
Patient AML |
RNAseq |
35868306 |
||
|
Healthy and AML |
RNAseq |
27526324 |
GSE74246 |
|
|
AML cell lines |
RNAseq |
31068700 |
||
|
TSU-1621-MT |
RNAseq |
26148230 |
GSE60477 |
SRR1552863, SRR1552864 |