E-MTAB-12238:Sample 357

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12238:Sample 357

text: gene all kit

characteristic: WGA

text: ArrayExpress

text: diagnosis

text: acute myeloid leukemia B phenotype

text: human

characteristic: common name

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

characteristic: organism part

text: FACS Aria

text: Homo sapiens

text: male

characteristic: subclone

text: Sample 357

text: 1:10 human CD45 positive out of mouse bone marrow 12L

characteristic: xenograft


E-MTAB-12238:Sample 358

status: PUBLIC

tag: attribute

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12238:Sample 358

tag: Namespace:Department of Molecular Cell Biology, Weizmann Institute of Science

characteristic: Submitter Id

text: gene all kit

text: ArrayExpress

characteristic: broker name

text: diagnosis

characteristic: clinical history

text: acute myeloid leukemia B phenotype

characteristic: clinical information

text: human

characteristic: date

text: Protocols: CD34+ cells were isolated from PB or BM (following mononuclear cell separation) of AML patients by positive selection using anti-human CD34 microbeads. Enriched CD34+ cells were sorted by FACSariaII (BD bioscience, CA, USA) into four subpopulations of HSPCs according to their surface markers and CD33 expression. The sorted fractions were collected either into Iscove's modified Dulbecco's medium (IMDM) +20% fetal bovine serum (FBS) (Biological Industries #02-023-1A) to be further used in the colony forming unit (CFU) assay or into PBS+2%FBS to be used in the xenotransplantation assay. The CFU assay was adjusted to the generation of single cell-derived subclones. HSPCs were seeded in 1% standard methylcellulose medium supplemented with 37% FBS, 1.2% bovine serum albumin (BSA), 1% L-glutamine, 10-6M b-mercaptoethanol, 1 IU/ml of human erythropoietin (EPO), 50 ng/ml of human stem cell factor (SCF), 25 ng/ml of human FLT3 ligand, 10 ng/ml of interleukin 3 (IL-3), 10 ng/ml of interleukin 6 (IL-6), 10 ng/ml of granulocytecolony stimulating factor (G-CSF), 5 ng/ml of granulocyte-macrophage colony-stimulating factor (GM-CSF), 10 ng/ml of human thrombopoietin (TPO), 100 IU ml penicillin and 100 mg/ml streptomycin. Colonies were counted after 14 days and each of them was picked under sterile conditions. Every individual colony was divided into two cell suspensions to perform both genotyping analysis and xenotransplantation into NSG mice. xenograft protocol: NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ (NSG) mice (The Jackson Laboratory, Bar Harbor, Maine, USA) were maintained and bred under specific pathogen-free conditions at the Biomedical Core Facility (Faculty of Medicine, the Technion, Haifa, Israel). Twenty-four hours prior to transplantation, 8-12-week-old female NSG mice were sub-lethally irradiated with 225 cGy. Primary human cells were intra-femorally injected. The total number of cells transplanted per mouse depended on the number of viable cells obtained from the BM/PB of a patient [ranged from 1 colony (a single cell-derived subclone) to 106 cells]. The animals were sacrificed 8-30 weeks after transplantation or if tumors developed in the injected knee. The BM was then harvested. Human engraftment was evaluated by flow cytometry using the following anti-human specific antibodies: anti-CD45-APC Cyanine7 (APC-Cy7) (BioLegend #304014 clone H130); anti-CD33-BV510 (BioLegend #366610); anti-CD34-BV421 (BioLegend #343610); anti-CD38-FITC (BD #555459); anti-CD15 APC (BD #551376); anti-CD19 PE-CY7 (BD #557835); Cell viability was obtained using Propidium Iodide - PI (BioLegend #421301). Analyses were performed using FlowJo software v.10 (Treestar, OR, USA), and the expression of markers was assessed and presented as the percentage of stained cells. The threshold for engraftment detection was 0.1% of human CD45+ cells. All flow cytometry analyses were done using an LSR II (BD Bioscience, CA, USA) or FACSariaII (BD Bioscience, CA, USA) device. Engraftment of >5% of hCD45+ cells with the major CD33+ population (>60% of the hCD45+ cells) was classified as overt leukemia; the presence of 0.1-5% of hCD45+ cells or the presence of >5% of hCD45+ cells with <60% of the CD33+ population in the hCD45+ cells was classified as non-overt leukemia; and the presence of <0.1% of human CD45+ (hCD45+) population was considered as non-engraftment. hCD45+ cells were sorted and underwent whole genome amplification (WGA) for further genotyping assays. CD34+ cells were isolated from PB or BM (following mononuclear cell separation) of AML patients by positive selection using anti-human CD34 microbeads. Enriched CD34+ cells were sorted by FACSariaII (BD bioscience, CA, USA) into four subpopulations of HSPCs according to their surface markers and CD33 expression. The sorted fractions were collected either into Iscove's modified Dulbecco's medium (IMDM) +20% fetal bovine serum (FBS) (Biological Industries #02-023-1A) to be further used in the colony forming unit (CFU) assay or into PBS+2%FBS to be used in the xenotransplantation assay. The CFU assay was adjusted to the generation of single cell-derived subclones. HSPCs were seeded in 1% standard methylcellulose medium supplemented with 37% FBS, 1.2% bovine serum albumin (BSA), 1% L-glutamine, 10-6M b-mercaptoethanol, 1 IU/ml of human erythropoietin (EPO), 50 ng/ml of human stem cell factor (SCF), 25 ng/ml of human FLT3 ligand, 10 ng/ml of interleukin 3 (IL-3), 10 ng/ml of interleukin 6 (IL-6), 10 ng/ml of granulocytecolony stimulating factor (G-CSF), 5 ng/ml of granulocyte-macrophage colony-stimulating factor (GM-CSF), 10 ng/ml of human thrombopoietin (TPO), 100 IU ml penicillin and 100 mg/ml streptomycin. Colonies were counted after 14 days and each of them was picked under sterile conditions. Every individual colony was divided into two cell suspensions to perform both genotyping analysis and xenotransplantation into NSG mice One µl of DNA template was added to a hybridization mix together with an MIP pool (final concentration of 0.05pM per probe) in 1x Ampligase buffer (Epicentre). The mix was incubated in a thermal cycler according to the following program: 98°C for 3 minutes, 85°C for 30 minutes, 60°C for 60 minutes and 56°C for 1 or 2 overnight incubations. The product was mixed with (final concentration in brackets): dNTPs (Larova, 15pM), Betaine (375 mM, Sigma-Aldrich,), NAD+ (1 mM, New England Biolabs), additional Ampligase buffer (0.5x), Ampligase (total of 1.25U, Epicentre) and Phusion HF (0.16U, New England Biolabs). The mix was incubated at 56°C for 60 minutes followed by 72°C for 20 minutes. Enzymatic digestion of linear probes was performed by adding Exonuclease I (4U, New England Biolabs) and Exonuclease III (25U, New England Biolabs). The mix was incubated at 37°C for 2 hours, followed by 80°C for 20 minutes. The final product was amplified using iProof HF Master Mix (Biorad). Samples were pooled and concentrated using AMPure XP beads (Beckman Coulter) at 1.3x volumetric concentration, size-selected (190-370bp) using Blue Pippin (Sage scientific), and sequenced in either NextSeq or Novaseq6000 (Illumina) 2X151bp paired-end run using custom primers as described in the past(Biezuner et al., 2022)

characteristic: description

text: adult

text: acute myeloid leukemia

characteristic: disease

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: blood

text: FACS Aria

characteristic: protocol

characteristic: sample id

text: Homo sapiens

text: male

characteristic: sex

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-; CD45 positive

characteristic: time

text: Sample 358

characteristic: title


E-MTAB-12238:Sample 359

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text: Department of Molecular Cell Biology, Weizmann Institute of Science

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12238:Sample 359

text: Repli G

characteristic: WGA

text: ArrayExpress

text: myeloid cell

text: diagnosis

text: acute myeloid leukemia B phenotype

text: human

characteristic: common name

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone marrow

characteristic: organism part

text: FACS Aria

text: Homo sapiens

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text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-

characteristic: subclone

text: Sample 359


E-MTAB-12238:Sample 36

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characteristic: broker name

text: common myeloid progenitor

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characteristic: clinical history

text: acute myeloid leukemia B phenotype

characteristic: clinical information

text: human

characteristic: date

characteristic: description

text: adult

text: acute myeloid leukemia

characteristic: disease

text: CD34+, CD38+, CD10-, CD7-, CD135(FLT3)+, CD45Ra-

characteristic: immunophenotype

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: FACS Aria - H4100 colony

characteristic: protocol

text: Homo sapiens

text: male

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-

text: Sample 36


E-MTAB-12238:Sample 360

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text: human

characteristic: common name

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text: acute myeloid leukemia

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text: Homo sapiens

text: bone marrow

text: FACS Aria

characteristic: sample id

text: Homo sapiens

text: male

characteristic: sex

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-

characteristic: time

text: Sample 360

characteristic: title


E-MTAB-12238:Sample 361

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characteristic: SRA accession

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characteristic: Submitter Id

text: Repli G

text: ArrayExpress

characteristic: broker name

text: diagnosis

characteristic: clinical history

text: acute myeloid leukemia

characteristic: clinical information

text: human

characteristic: date

characteristic: description

text: adult

text: acute myeloid leukemia

characteristic: disease

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

characteristic: organism part

text: FACS Aria

text: Homo sapiens

text: male

text: NPM1+ FLT3-ITD+; CD45 positive

characteristic: subclone

text: Sample 361

text: human CD45 positive out of mouse bone marrow 72

characteristic: xenograft


E-MTAB-12238:Sample 362

characteristic: ENA-CHECKLIST

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text: Repli G

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text: ArrayExpress

text: diagnosis

text: acute myeloid leukemia

text: human

characteristic: common name

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

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text: Homo sapiens

text: Homo sapiens

text: blood

text: FACS Aria

characteristic: protocol

characteristic: sample id

text: Homo sapiens

text: male

characteristic: sex

text: NPM1+ FLT3-ITD+; CD45 positive

text: Sample 362


E-MTAB-12238:Sample 363

characteristic: INSDC last update

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text: E-MTAB-12238:Sample 363

characteristic: Submitter Id

text: Repli G

text: ArrayExpress

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text: common lymphoid progenitor

text: diagnosis

characteristic: clinical history

text: acute myeloid leukemia

characteristic: clinical information

text: human

characteristic: date

characteristic: description

text: adult

text: acute myeloid leukemia

characteristic: disease

text: CD34+, CD38-,CD90+/-, CD45Ra+

characteristic: immunophenotype

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: FACS Aria

text: Homo sapiens

text: male

text: NPM1+ FLT3-ITD+

characteristic: time

text: Sample 363

characteristic: title

text: 1:10 human CD45 positive out of mouse bone marrow 72


E-MTAB-12238:Sample 364

characteristic: ENA-CHECKLIST

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text: ArrayExpress

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text: diagnosis

text: acute myeloid leukemia

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characteristic: common name

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

text: CD34+, CD38-,CD90+/-, CD45Ra+

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: FACS Aria

characteristic: protocol

text: Homo sapiens

text: male

text: NPM1+ FLT3-ITD+

characteristic: subclone

text: Sample 364

characteristic: xenograft


E-MTAB-12238:Sample 365

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text: E-MTAB-12238:Sample 365

characteristic: Submitter Id

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text: ArrayExpress

characteristic: broker name

text: granulocyte monocyte progenitor cell

text: diagnosis

characteristic: clinical history

text: acute myeloid leukemia B phenotype

characteristic: clinical information

text: human

characteristic: date

characteristic: description

text: adult

text: acute myeloid leukemia

characteristic: disease

text: CD34+, CD38+, CD10-, CD7-, CD135(FLT3)+, CD45Ra+

characteristic: immunophenotype

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone marrow

text: FACS Aria

characteristic: sample id

text: Homo sapiens

text: male

characteristic: sex

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-

text: Sample 365


E-MTAB-12238:Sample 366

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

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characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12238:Sample 366

text: Repli G

characteristic: WGA

text: ArrayExpress

text: granulocyte monocyte progenitor cell

text: diagnosis

text: acute myeloid leukemia B phenotype

text: human

characteristic: common name

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: bone marrow

characteristic: organism part

text: FACS Aria

characteristic: protocol

text: Homo sapiens

text: male

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-

characteristic: time

text: Sample 366

characteristic: title


E-MTAB-12238:Sample 367

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12238:Sample 367

characteristic: Submitter Id

text: Repli G

text: ArrayExpress

characteristic: broker name

text: relapse

characteristic: clinical history

text: acute myeloid leukemia B phenotype

characteristic: clinical information

text: human

characteristic: date

characteristic: description

text: adult

text: acute myeloid leukemia

characteristic: disease

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: FACS Aria

text: Homo sapiens

text: male

characteristic: subclone

text: Sample 367

text: human CD45 positive out of mouse bone marrow 19

characteristic: xenograft


E-MTAB-12238:Sample 368

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12238:Sample 368

text: Repli G

characteristic: WGA

text: ArrayExpress

text: relapse

text: acute myeloid leukemia B phenotype

text: human

characteristic: common name

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: FACS Aria

characteristic: sample id

text: Homo sapiens

text: male

characteristic: sex

text: Sample 368


E-MTAB-12238:Sample 369

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12238:Sample 369

characteristic: Submitter Id

text: Repli G

text: ArrayExpress

characteristic: broker name

text: common myeloid progenitor

text: relapse

characteristic: clinical history

text: acute myeloid leukemia B phenotype

characteristic: clinical information

text: human

characteristic: date

characteristic: description

text: adult

text: acute myeloid leukemia

characteristic: disease

characteristic: immunophenotype

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: FACS Aria

characteristic: protocol

text: Homo sapiens

text: male

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-

characteristic: time

text: Sample 369

characteristic: title


E-MTAB-12238:Sample 37

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12238:Sample 37

text: Repli G

characteristic: WGA

text: ArrayExpress

characteristic: cell count

text: relapse

text: acute myeloid leukemia B phenotype

text: human

characteristic: common name

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

characteristic: organism part

text: FACS Aria

text: Homo sapiens

text: male

characteristic: subclone

text: Sample 37

text: human CD45 positive out of mouse bone marrow 21

characteristic: xenograft


E-MTAB-12238:Sample 370

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12238:Sample 370

characteristic: Submitter Id

text: Repli G

text: ArrayExpress

characteristic: broker name

text: common myeloid progenitor

text: relapse

characteristic: clinical history

text: acute myeloid leukemia B phenotype

characteristic: clinical information

text: human

characteristic: date

characteristic: description

text: adult

text: acute myeloid leukemia

characteristic: disease

characteristic: immunophenotype

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: FACS Aria

characteristic: protocol

characteristic: sample id

text: Homo sapiens

text: male

characteristic: sex

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-

characteristic: time

text: Sample 370


E-MTAB-12238:Sample 371

characteristic: ENA-CHECKLIST

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characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12238:Sample 371

text: Repli G

characteristic: WGA

text: ArrayExpress

text: granulocyte monocyte progenitor cell

text: diagnosis

text: acute myeloid leukemia B phenotype

text: human

characteristic: common name

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone marrow

characteristic: organism part

text: FACS Aria

text: Homo sapiens

text: male

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-

characteristic: subclone

text: Sample 371

characteristic: title


E-MTAB-12238:Sample 372

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12238:Sample 372

characteristic: Submitter Id

text: Repli G

text: ArrayExpress

characteristic: broker name

text: granulocyte monocyte progenitor cell

text: diagnosis

characteristic: clinical history

text: acute myeloid leukemia B phenotype

characteristic: clinical information

text: human

characteristic: date

characteristic: description

text: adult

text: acute myeloid leukemia

characteristic: disease

characteristic: immunophenotype

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: FACS Aria

characteristic: protocol

characteristic: sample id

text: Homo sapiens

text: male

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-

text: Sample 372


E-MTAB-12238:Sample 373

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12238:Sample 373

text: Repli G

characteristic: WGA

text: ArrayExpress

text: common myeloid progenitor

text: relapse

text: acute myeloid leukemia B phenotype

text: human

characteristic: common name

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: FACS Aria

text: Homo sapiens

text: male

characteristic: sex

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-

characteristic: time

text: Sample 373

text: 1:10 human CD45 positive out of mouse bone marrow 19

characteristic: xenograft


E-MTAB-12238:Sample 374

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12238:Sample 374

characteristic: Submitter Id

text: Repli G

text: ArrayExpress

characteristic: broker name

text: common myeloid progenitor

text: relapse

characteristic: clinical history

text: acute myeloid leukemia B phenotype

characteristic: clinical information

text: human

characteristic: date

characteristic: description

text: adult

text: acute myeloid leukemia

characteristic: disease

characteristic: immunophenotype

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: FACS Aria

text: Homo sapiens

text: male

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-

characteristic: subclone

text: Sample 374

characteristic: title


E-MTAB-12238:Sample 375

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12238:Sample 375

text: Repli G

characteristic: WGA

text: ArrayExpress

text: B cell

text: diagnosis

text: acute myeloid leukemia B phenotype

text: human

characteristic: common name

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone marrow

text: FACS Aria

characteristic: protocol

characteristic: sample id

text: Homo sapiens

text: male

characteristic: sex

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-

text: Sample 375


E-MTAB-12238:Sample 376

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12238:Sample 376

characteristic: Submitter Id

text: Repli G

text: ArrayExpress

characteristic: broker name

text: B cell

text: diagnosis

characteristic: clinical history

text: acute myeloid leukemia B phenotype

characteristic: clinical information

text: human

characteristic: date

characteristic: description

text: adult

text: acute myeloid leukemia

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: bone marrow

characteristic: organism part

text: FACS Aria

text: Homo sapiens

text: male

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-

characteristic: time

text: Sample 376


E-MTAB-12238:Sample 377

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12238:Sample 377

text: Repli G

characteristic: WGA

text: ArrayExpress

text: diagnosis

text: acute myeloid leukemia

text: human

characteristic: common name

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: blood

text: FACS Aria

text: Homo sapiens

text: male

text: NPM1+ FLT3-ITD+; CD45 negative

characteristic: subclone

text: Sample 377

characteristic: title

text: mouse bone marrow 72 CD45- for negative control

characteristic: xenograft


E-MTAB-12238:Sample 378

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12238:Sample 378

characteristic: Submitter Id

text: Repli G

text: ArrayExpress

characteristic: broker name

text: diagnosis

characteristic: clinical history

text: acute myeloid leukemia

characteristic: clinical information

text: human

characteristic: date

characteristic: description

text: adult

text: acute myeloid leukemia

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: FACS Aria

characteristic: protocol

characteristic: sample id

text: Homo sapiens

text: male

characteristic: sex

text: NPM1+ FLT3-ITD+; CD45 negative

text: Sample 378


E-MTAB-12238:Sample 379

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12238:Sample 379

text: Repli G

characteristic: WGA

text: ArrayExpress

text: diagnosis

text: acute myeloid leukemia

text: human

characteristic: common name

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: disease

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: FACS Aria

text: Homo sapiens

text: male

text: NPM1+ FLT3-ITD+; CD45 negative

characteristic: time

text: Sample 379

text: 1:10 mouse bone marrow 72 CD45 negative for negative control


E-MTAB-12238:Sample 38

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12238:Sample 38

characteristic: Submitter Id

text: Repli G

text: ArrayExpress

characteristic: broker name

characteristic: cell count

text: relapse

characteristic: clinical history

text: acute myeloid leukemia B phenotype

characteristic: clinical information

text: human

characteristic: date

characteristic: description

text: adult

text: acute myeloid leukemia

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: FACS Aria

text: Homo sapiens

text: male

characteristic: subclone

text: Sample 38

characteristic: title

characteristic: xenograft


E-MTAB-12238:Sample 380

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12238:Sample 380

text: Repli G

characteristic: WGA

text: ArrayExpress

text: diagnosis

text: acute myeloid leukemia

text: human

characteristic: common name

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: disease

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: blood

text: FACS Aria

characteristic: protocol

characteristic: sample id

text: Homo sapiens

text: male

characteristic: sex

text: NPM1+ FLT3-ITD+; CD45 negative

text: Sample 380


E-MTAB-12238:Sample 381

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12238:Sample 381

characteristic: Submitter Id

text: Repli G

text: ArrayExpress

characteristic: broker name

text: common myeloid progenitor

text: diagnosis

characteristic: clinical history

text: acute myeloid leukemia B phenotype

characteristic: clinical information

text: human

characteristic: date

characteristic: description

text: adult

text: acute myeloid leukemia

characteristic: immunophenotype

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone marrow

characteristic: organism part

text: FACS Aria

text: Homo sapiens

text: male

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-

characteristic: subclone

characteristic: time

text: Sample 381


E-MTAB-12238:Sample 382

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12238:Sample 382

text: Repli G

characteristic: WGA

text: ArrayExpress

text: common myeloid progenitor

text: diagnosis

text: acute myeloid leukemia B phenotype

text: human

characteristic: common name

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: disease

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: FACS Aria

characteristic: protocol

text: Homo sapiens

text: male

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-

text: Sample 382

characteristic: title


E-MTAB-12238:Sample 383

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12238:Sample 383

characteristic: Submitter Id

text: Repli G

text: ArrayExpress

characteristic: broker name

text: relapse

characteristic: clinical history

text: acute myeloid leukemia B phenotype

characteristic: clinical information

text: human

characteristic: date

characteristic: description

text: adult

text: acute myeloid leukemia

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: FACS Aria

characteristic: sample id

text: Homo sapiens

text: male

characteristic: sex

text: Sample 383

text: human CD45 positive out of mouse bone marrow 20

characteristic: xenograft


E-MTAB-12238:Sample 384

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12238:Sample 384

text: Repli G

characteristic: WGA

text: ArrayExpress

text: relapse

text: acute myeloid leukemia B phenotype

text: human

characteristic: common name

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: FACS Aria

text: Homo sapiens

text: male

characteristic: subclone

characteristic: time

text: Sample 384


E-MTAB-12238:Sample 385

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12238:Sample 385

characteristic: Submitter Id

text: Repli G

text: ArrayExpress

characteristic: broker name

text: common myeloid progenitor

text: diagnosis

characteristic: clinical history

text: acute myeloid leukemia B phenotype

characteristic: clinical information

text: human

characteristic: date

characteristic: description

text: adult

text: acute myeloid leukemia

characteristic: immunophenotype

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone marrow

text: FACS Aria

characteristic: protocol

text: Homo sapiens

text: male

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-

text: Sample 385

characteristic: title


E-MTAB-12238:Sample 386

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12238:Sample 386

text: Repli G

characteristic: WGA

text: ArrayExpress

text: common myeloid progenitor

text: diagnosis

text: acute myeloid leukemia B phenotype

text: human

characteristic: common name

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: bone marrow

characteristic: organism part

text: FACS Aria

characteristic: sample id

text: Homo sapiens

text: male

characteristic: sex

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-

text: Sample 386


E-MTAB-12238:Sample 387

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12238:Sample 387

characteristic: Submitter Id

text: Repli G

text: ArrayExpress

characteristic: broker name

text: common lymphoid progenitor

text: relapse

characteristic: clinical history

text: acute myeloid leukemia B phenotype

characteristic: clinical information

text: human

characteristic: date

characteristic: description

text: adult

text: acute myeloid leukemia

text: CD34+, CD38-,CD90+/-, CD45Ra+

characteristic: immunophenotype

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: blood

text: FACS Aria

text: Homo sapiens

text: male

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-

characteristic: subclone

characteristic: time

text: Sample 387

text: 1:10 human CD45 positive out of mouse bone marrow 20

characteristic: xenograft


E-MTAB-12238:Sample 388

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12238:Sample 388

text: Repli G

characteristic: WGA

text: ArrayExpress

text: common lymphoid progenitor

text: relapse

text: acute myeloid leukemia B phenotype

text: human

characteristic: common name

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: disease

text: CD34+, CD38-,CD90+/-, CD45Ra+

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

characteristic: organism part

text: FACS Aria

characteristic: protocol

text: Homo sapiens

text: male

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-

text: Sample 388

characteristic: title


E-MTAB-12238:Sample 389

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12238:Sample 389

characteristic: Submitter Id

text: Repli G

text: ArrayExpress

characteristic: broker name

text: immature B cell

text: diagnosis

characteristic: clinical history

text: acute myeloid leukemia B phenotype

characteristic: clinical information

text: human

characteristic: date

characteristic: description

text: adult

text: acute myeloid leukemia

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: FACS Aria

characteristic: sample id

text: Homo sapiens

text: male

characteristic: sex

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-

characteristic: subclone

text: Sample 389


E-MTAB-12238:Sample 39

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12238:Sample 39

text: Repli G

characteristic: WGA

text: ArrayExpress

text: diagnosis

text: acute myeloid leukemia B phenotype

text: human

characteristic: common name

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: disease

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: FACS Aria

text: Homo sapiens

text: male

characteristic: time

text: Sample 39

text: human CD45 positive out of mouse bone marrow 83

characteristic: xenograft


E-MTAB-12238:Sample 390

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12238:Sample 390

characteristic: Submitter Id

text: Repli G

text: ArrayExpress

characteristic: broker name

text: immature B cell

text: diagnosis

characteristic: clinical history

text: acute myeloid leukemia B phenotype

characteristic: clinical information

text: human

characteristic: date

characteristic: description

text: adult

text: acute myeloid leukemia

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: bone marrow

characteristic: organism part

text: FACS Aria

characteristic: protocol

text: Homo sapiens

text: male

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-

text: Sample 390

characteristic: title


E-MTAB-12238:Sample 391

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12238:Sample 391

text: ArrayExpress

text: diagnosis

text: acute myeloid leukemia B phenotype

text: human

characteristic: common name

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: DNA Purification from BM

characteristic: sample id

text: Homo sapiens

text: male

characteristic: sex

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-

characteristic: subclone

text: Sample 391


E-MTAB-12238:Sample 392

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12238:Sample 392

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: diagnosis

characteristic: clinical history

text: acute myeloid leukemia B phenotype

characteristic: clinical information

text: human

characteristic: date

characteristic: description

text: adult

text: acute myeloid leukemia

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone marrow

text: DNA Purification from BM

text: Homo sapiens

text: male

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-

characteristic: time

text: Sample 392


E-MTAB-12238:Sample 393

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12238:Sample 393

text: Repli G

characteristic: WGA

text: ArrayExpress

text: diagnosis

text: acute myeloid leukemia

text: human

characteristic: common name

text: adult

text: acute myeloid leukemia

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: FACS Aria

characteristic: protocol

text: Homo sapiens

text: male

text: NPM1+ FLT3-ITD+; CD45 positive

text: Sample 393

characteristic: title

text: human CD45 positive out of mouse bone marrow 73

characteristic: xenograft


E-MTAB-12238:Sample 394

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12238:Sample 394

characteristic: Submitter Id

text: Repli G

text: ArrayExpress

characteristic: broker name

text: diagnosis

characteristic: clinical history

text: acute myeloid leukemia

characteristic: clinical information

text: human

characteristic: date

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: blood

text: FACS Aria

characteristic: sample id

text: Homo sapiens

text: male

characteristic: sex

text: NPM1+ FLT3-ITD+; CD45 positive

characteristic: subclone

text: Sample 394


E-MTAB-12238:Sample 395

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12238:Sample 395

text: Repli G

characteristic: WGA

text: ArrayExpress

text: common lymphoid progenitor

text: diagnosis

text: acute myeloid leukemia

text: human

characteristic: common name

characteristic: description

text: adult

text: acute myeloid leukemia

text: CD34+, CD38-,CD90+/-, CD45Ra+

characteristic: immunophenotype

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

characteristic: organism part

text: FACS Aria

text: Homo sapiens

text: male

text: NPM1+ FLT3-ITD+

characteristic: time

text: Sample 395

text: 1:10 human CD45 positive out of mouse bone marrow 73


E-MTAB-12238:Sample 396

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12238:Sample 396

characteristic: Submitter Id

text: Repli G

text: ArrayExpress

characteristic: broker name

text: common lymphoid progenitor

text: diagnosis

characteristic: clinical history

text: acute myeloid leukemia

characteristic: clinical information

text: human

characteristic: date

text: Protocols: CD34+ cells were isolated from PB or BM (following mononuclear cell separation) of AML patients by positive selection using anti-human CD34 microbeads. Enriched CD34+ cells were sorted by FACSariaII (BD bioscience, CA, USA) into four subpopulations of HSPCs according to their surface markers and CD33 expression. The sorted fractions were collected either into Iscove's modified Dulbecco's medium (IMDM) +20% fetal bovine serum (FBS) (Biological Industries #02-023-1A) to be further used in the colony forming unit (CFU) assay or into PBS+2%FBS to be used in the xenotransplantation assay. The CFU assay was adjusted to the generation of single cell-derived subclones. HSPCs were seeded in 1% standard methylcellulose medium supplemented with 37% FBS, 1.2% bovine serum albumin (BSA), 1% L-glutamine, 10-6M b-mercaptoethanol, 1 IU/ml of human erythropoietin (EPO), 50 ng/ml of human stem cell factor (SCF), 25 ng/ml of human FLT3 ligand, 10 ng/ml of interleukin 3 (IL-3), 10 ng/ml of interleukin 6 (IL-6), 10 ng/ml of granulocytecolony stimulating factor (G-CSF), 5 ng/ml of granulocyte-macrophage colony-stimulating factor (GM-CSF), 10 ng/ml of human thrombopoietin (TPO), 100 IU ml penicillin and 100 mg/ml streptomycin. Colonies were counted after 14 days and each of them was picked under sterile conditions. Every individual colony was divided into two cell suspensions to perform both genotyping analysis and xenotransplantation into NSG mice. xenograft protocol: NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ (NSG) mice (The Jackson Laboratory, Bar Harbor, Maine, USA) were maintained and bred under specific pathogen-free conditions at the Biomedical Core Facility (Faculty of Medicine, the Technion, Haifa, Israel). Twenty-four hours prior to transplantation, 8-12-week-old female NSG mice were sub-lethally irradiated with 225 cGy. Primary human cells were intra-femorally injected. The total number of cells transplanted per mouse depended on the number of viable cells obtained from the BM/PB of a patient [ranged from 1 colony (a single cell-derived subclone) to 106 cells]. The animals were sacrificed 8-30 weeks after transplantation or if tumors developed in the injected knee. The BM was then harvested. Human engraftment was evaluated by flow cytometry using the following anti-human specific antibodies: anti-CD45-APC Cyanine7 (APC-Cy7) (BioLegend #304014 clone H130); anti-CD33-BV510 (BioLegend #366610); anti-CD34-BV421 (BioLegend #343610); anti-CD38-FITC (BD #555459); anti-CD15 APC (BD #551376); anti-CD19 PE-CY7 (BD #557835); Cell viability was obtained using Propidium Iodide - PI (BioLegend #421301). Analyses were performed using FlowJo software v.10 (Treestar, OR, USA), and the expression of markers was assessed and presented as the percentage of stained cells. The threshold for engraftment detection was 0.1% of human CD45+ cells. All flow cytometry analyses were done using an LSR II (BD Bioscience, CA, USA) or FACSariaII (BD Bioscience, CA, USA) device. Engraftment of >5% of hCD45+ cells with the major CD33+ population (>60% of the hCD45+ cells) was classified as overt leukemia; the presence of 0.1-5% of hCD45+ cells or the presence of >5% of hCD45+ cells with <60% of the CD33+ population in the hCD45+ cells was classified as non-overt leukemia; and the presence of <0.1% of human CD45+ (hCD45+) population was considered as non-engraftment. hCD45+ cells were sorted and underwent whole genome amplification (WGA) for further genotyping assays. CD34+ cells were isolated from PB or BM (following mononuclear cell separation) of AML patients by positive selection using anti-human CD34 microbeads. Enriched CD34+ cells were sorted by FACSariaII (BD bioscience, CA, USA) into four subpopulations of HSPCs according to their surface markers and CD33 expression. The sorted fractions were collected either into Iscove's modified Dulbecco's medium (IMDM) +20% fetal bovine serum (FBS) (Biological Industries #02-023-1A) to be further used in the colony forming unit (CFU) assay or into PBS+2%FBS to be used in the xenotransplantation assay. The CFU assay was adjusted to the generation of single cell-derived subclones. HSPCs were seeded in 1% standard methylcellulose medium supplemented with 37% FBS, 1.2% bovine serum albumin (BSA), 1% L-glutamine, 10-6M b-mercaptoethanol, 1 IU/ml of human erythropoietin (EPO), 50 ng/ml of human stem cell factor (SCF), 25 ng/ml of human FLT3 ligand, 10 ng/ml of interleukin 3 (IL-3), 10 ng/ml of interleukin 6 (IL-6), 10 ng/ml of granulocytecolony stimulating factor (G-CSF), 5 ng/ml of granulocyte-macrophage colony-stimulating factor (GM-CSF), 10 ng/ml of human thrombopoietin (TPO), 100 IU ml penicillin and 100 mg/ml streptomycin. Colonies were counted after 14 days and each of them was picked under sterile conditions. Every individual colony was divided into two cell suspensions to perform both genotyping analysis and xenotransplantation into NSG mice One µl of DNA template was added to a hybridization mix together with an MIP pool (final concentration of 0.05pM per probe) in 1x Ampligase buffer (Epicentre). The mix was incubated in a thermal cycler according to the following program: 98°C for 3 minutes, 85°C for 30 minutes, 60°C for 60 minutes and 56°C for 1 or 2 overnight incubations. The product was mixed with (final concentration in brackets): dNTPs (Larova, 15pM), Betaine (375 mM, Sigma-Aldrich,), NAD+ (1 mM, New England Biolabs), additional Ampligase buffer (0.5x), Ampligase (total of 1.25U, Epicentre) and Phusion HF (0.16U, New England Biolabs). The mix was incubated at 56°C for 60 minutes followed by 72°C for 20 minutes. Enzymatic digestion of linear probes was performed by adding Exonuclease I (4U, New England Biolabs) and Exonuclease III (25U, New England Biolabs). The mix was incubated at 37°C for 2 hours, followed by 80°C for 20 minutes. The final product was amplified using iProof HF Master Mix (Biorad). Samples were pooled and concentrated using AMPure XP beads (Beckman Coulter) at 1.3x volumetric concentration, size-selected (190-370bp) using Blue Pippin (Sage scientific), and sequenced in either NextSeq or Novaseq6000 (Illumina) 2X151bp paired-end run using custom primers as described in the past(Biezuner et al., 2022)

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: disease

text: CD34+, CD38-,CD90+/-, CD45Ra+

text: Homo sapiens

text: Homo sapiens

text: blood

text: FACS Aria

characteristic: protocol

characteristic: sample id

text: Homo sapiens

text: male

text: NPM1+ FLT3-ITD+

text: Sample 396

characteristic: title

characteristic: xenograft


E-MTAB-12238:Sample 397

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12238:Sample 397

text: Repli G

characteristic: WGA

text: ArrayExpress

text: hematopoietic multipotent progenitor cell

text: diagnosis

text: acute myeloid leukemia B phenotype

text: human

characteristic: common name

characteristic: description

text: adult

text: acute myeloid leukemia

text: CD34+, CD38-,CD90+/-, CD45Ra-

characteristic: immunophenotype

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone marrow

text: FACS Aria

text: Homo sapiens

text: male

characteristic: sex

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-

characteristic: subclone

text: Sample 397


E-MTAB-12238:Sample 398

text: Department of Molecular Cell Biology, Weizmann Institute of Science

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12238:Sample 398

characteristic: Submitter Id

text: Repli G

text: ArrayExpress

characteristic: broker name

text: diagnosis

characteristic: clinical history

text: acute myeloid leukemia B phenotype

characteristic: clinical information

text: human

characteristic: date

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: disease

text: CD34+, CD38-,CD90+/-, CD45Ra-

text: Homo sapiens

text: Homo sapiens

text: bone marrow

characteristic: organism part

text: FACS Aria

characteristic: protocol

characteristic: sample id

text: Homo sapiens

text: male

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-

characteristic: time

text: Sample 398


E-MTAB-12238:Sample 399

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12238:Sample 399

text: Repli G

characteristic: WGA

text: ArrayExpress

text: diagnosis

text: acute myeloid leukemia B phenotype

text: human

characteristic: common name

characteristic: description

text: adult

text: acute myeloid leukemia

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: FACS Aria

text: Homo sapiens

text: male

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-; CD45 positive

text: Sample 399

characteristic: title

text: human CD45 positive out of mouse bone marrow 23

characteristic: xenograft


E-MTAB-12238:Sample 4

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12238:Sample 4

characteristic: Submitter Id

text: Repli G

text: ArrayExpress

characteristic: broker name

text: diagnosis

characteristic: clinical history

text: acute myeloid leukemia B phenotype

characteristic: clinical information

text: human

characteristic: date

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: bone marrow

characteristic: organism part

text: FACS Aria

text: Homo sapiens

text: male

characteristic: sex

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-; CD34 positive ; CD34 positive

characteristic: subclone

text: Sample 4


E-MTAB-12238:Sample 40

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12238:Sample 40

text: Repli G

characteristic: WGA

text: ArrayExpress

text: diagnosis

text: acute myeloid leukemia B phenotype

text: human

characteristic: common name

characteristic: description

text: adult

text: acute myeloid leukemia

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: blood

text: FACS Aria

characteristic: protocol

characteristic: sample id

text: Homo sapiens

text: male

characteristic: time

text: Sample 40


E-MTAB-12238:Sample 400

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12238:Sample 400

characteristic: Submitter Id

text: Repli G

text: ArrayExpress

characteristic: broker name

text: diagnosis

characteristic: clinical history

text: acute myeloid leukemia B phenotype

characteristic: clinical information

text: human

characteristic: date

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: disease

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: FACS Aria

text: Homo sapiens

text: male

text: Sample 400

characteristic: title

characteristic: xenograft


E-MTAB-12238:Sample 401

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12238:Sample 401

text: Repli G

characteristic: WGA

text: ArrayExpress

text: diagnosis

text: acute myeloid leukemia B phenotype

text: human

characteristic: common name

characteristic: description

text: adult

text: acute myeloid leukemia

text: CD34+, CD38-,CD90+/-, CD45Ra-

characteristic: immunophenotype

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: bone marrow

characteristic: organism part

text: FACS Aria

text: Homo sapiens

text: male

characteristic: sex

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-

characteristic: subclone

text: Sample 401


E-MTAB-12238:Sample 402

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12238:Sample 402

characteristic: Submitter Id

text: Repli G

text: ArrayExpress

characteristic: broker name

text: diagnosis

characteristic: clinical history

text: acute myeloid leukemia B phenotype

characteristic: clinical information

text: human

characteristic: date

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: disease

text: CD34+, CD38-,CD90+/-, CD45Ra-

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone marrow

text: FACS Aria

characteristic: protocol

characteristic: sample id

text: Homo sapiens

text: male

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-

characteristic: time

text: Sample 402


E-MTAB-12238:Sample 403

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12238:Sample 403

text: Repli G

characteristic: WGA

text: ArrayExpress

text: diagnosis

text: acute myeloid leukemia B phenotype

text: human

characteristic: common name

characteristic: description

text: adult

text: acute myeloid leukemia

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: FACS Aria

text: Homo sapiens

text: male

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-; CD34 positive

text: Sample 403

characteristic: title

text: 1:10 human CD45 positive out of mouse bone marrow 23

characteristic: xenograft


E-MTAB-12238:Sample 404

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12238:Sample 404

characteristic: Submitter Id

text: Repli G

text: ArrayExpress

characteristic: broker name

text: diagnosis

characteristic: clinical history

text: acute myeloid leukemia B phenotype

characteristic: clinical information

text: human

characteristic: date

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: disease

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: FACS Aria

text: Homo sapiens

text: male

characteristic: sex

characteristic: subclone

text: Sample 404


E-MTAB-12238:Sample 405

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12238:Sample 405

text: Repli G

characteristic: WGA

text: ArrayExpress

text: diagnosis

text: acute myeloid leukemia B phenotype

text: human

characteristic: common name

characteristic: description

text: adult

text: acute myeloid leukemia

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: FACS Aria

characteristic: protocol

characteristic: sample id

text: Homo sapiens

text: male

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-; CD34 negative; CD34 negative

characteristic: time

text: Sample 405


E-MTAB-12238:Sample 406

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12238:Sample 406

characteristic: Submitter Id

text: Repli G

text: ArrayExpress

characteristic: broker name

text: diagnosis

characteristic: clinical history

text: acute myeloid leukemia B phenotype

characteristic: clinical information

text: human

characteristic: date

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: bone marrow

characteristic: organism part

text: FACS Aria

text: Homo sapiens

text: male

text: Sample 406

characteristic: title


E-MTAB-12238:Sample 407

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12238:Sample 407

text: Repli G

characteristic: WGA

text: ArrayExpress

text: diagnosis

text: acute myeloid leukemia

text: human

characteristic: common name

characteristic: description

text: adult

text: acute myeloid leukemia

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: FACS Aria

text: Homo sapiens

text: male

characteristic: sex

text: NPM1+ FLT3-ITD+; CD45 positive

characteristic: subclone

text: Sample 407

text: human CD45 positive out of mouse bone marrow 74

characteristic: xenograft


E-MTAB-12238:Sample 408

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12238:Sample 408

characteristic: Submitter Id

text: Repli G

text: ArrayExpress

characteristic: broker name

text: diagnosis

characteristic: clinical history

text: acute myeloid leukemia

characteristic: clinical information

text: human

characteristic: date

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: blood

text: FACS Aria

characteristic: protocol

characteristic: sample id

text: Homo sapiens

text: male

text: NPM1+ FLT3-ITD+; CD45 positive

characteristic: time

text: Sample 408


E-MTAB-12238:Sample 409

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12238:Sample 409

text: Repli G

characteristic: WGA

text: ArrayExpress

text: granulocyte monocyte progenitor cell

text: diagnosis

text: acute myeloid leukemia

text: human

characteristic: common name

characteristic: description

text: adult

text: acute myeloid leukemia

characteristic: disease

text: CD34+, CD38+, CD10-, CD7-, CD135(FLT3)+, CD45Ra+

characteristic: immunophenotype

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

characteristic: organism part

text: FACS Aria

text: Homo sapiens

text: male

text: NPM1+ FLT3-ITD+

text: Sample 409

characteristic: title

text: 1:10 human CD45 positive out of mouse bone marrow 74


E-MTAB-12238:Sample 41

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12238:Sample 41

characteristic: Submitter Id

text: Repli G

text: ArrayExpress

characteristic: broker name

text: common myeloid progenitor

text: diagnosis

characteristic: clinical history

text: acute myeloid leukemia B phenotype

characteristic: clinical information

text: human

characteristic: date

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

text: CD34+, CD38+, CD10-, CD7-, CD135(FLT3)+, CD45Ra-

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: FACS Aria - H4100 colony

characteristic: protocol

text: Homo sapiens

text: male

characteristic: sex

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-

characteristic: subclone

text: Sample 41


E-MTAB-12238:Sample 410

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12238:Sample 410

text: Repli G

characteristic: WGA

text: ArrayExpress

text: granulocyte monocyte progenitor cell

text: diagnosis

text: acute myeloid leukemia

text: human

characteristic: common name

characteristic: description

text: adult

text: acute myeloid leukemia

characteristic: disease

characteristic: immunophenotype

text: Homo sapiens

text: Homo sapiens

text: blood

text: FACS Aria

characteristic: sample id

text: Homo sapiens

text: male

text: NPM1+ FLT3-ITD+

characteristic: time

text: Sample 410

characteristic: xenograft


E-MTAB-12238:Sample 411

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12238:Sample 411

characteristic: Submitter Id

text: Repli G

text: ArrayExpress

characteristic: broker name

text: common myeloid progenitor

text: diagnosis

characteristic: clinical history

text: acute myeloid leukemia B phenotype

characteristic: clinical information

text: human

characteristic: date

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone marrow

characteristic: organism part

text: FACS Aria

characteristic: protocol

text: Homo sapiens

text: male

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-

text: Sample 411

characteristic: title


E-MTAB-12238:Sample 412

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12238:Sample 412

text: Repli G

characteristic: WGA

text: ArrayExpress

text: common myeloid progenitor

text: diagnosis

text: acute myeloid leukemia B phenotype

text: human

characteristic: common name

characteristic: description

text: adult

text: acute myeloid leukemia

characteristic: disease

characteristic: immunophenotype

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: FACS Aria

characteristic: sample id

text: Homo sapiens

text: male

characteristic: sex

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-

characteristic: subclone

text: Sample 412


E-MTAB-12238:Sample 414

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12238:Sample 414

characteristic: Submitter Id

text: Repli G

text: ArrayExpress

characteristic: broker name

text: common myeloid progenitor

text: relapse

characteristic: clinical history

text: acute myeloid leukemia B phenotype

characteristic: clinical information

text: human

characteristic: date

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone marrow

characteristic: organism part

text: FACS Aria

text: Homo sapiens

text: male

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-

characteristic: time

text: Sample 414


E-MTAB-12238:Sample 415

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12238:Sample 415

text: Repli G

characteristic: WGA

text: ArrayExpress

text: relapse

text: acute myeloid leukemia B phenotype

text: human

characteristic: common name

characteristic: description

text: adult

text: acute myeloid leukemia

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: blood

text: FACS Aria

characteristic: protocol

text: Homo sapiens

text: male

text: Sample 415

characteristic: title

text: human CD45 positive out of mouse bone marrow 24

characteristic: xenograft


E-MTAB-12238:Sample 416

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12238:Sample 416

characteristic: Submitter Id

text: Repli G

text: ArrayExpress

characteristic: broker name

text: relapse

characteristic: clinical history

text: acute myeloid leukemia B phenotype

characteristic: clinical information

text: human

characteristic: date

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: blood

text: FACS Aria

characteristic: sample id

text: Homo sapiens

text: male

characteristic: sex

characteristic: subclone

text: Sample 416


E-MTAB-12238:Sample 417

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12238:Sample 417

text: Repli G

characteristic: WGA

text: ArrayExpress

text: common myeloid progenitor

text: diagnosis

text: acute myeloid leukemia B phenotype

text: human

characteristic: common name

characteristic: description

text: adult

text: acute myeloid leukemia

characteristic: disease

characteristic: immunophenotype

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone marrow

characteristic: organism part

text: FACS Aria

text: Homo sapiens

text: male

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-

characteristic: time

text: Sample 417


E-MTAB-12238:Sample 418

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12238:Sample 418

characteristic: Submitter Id

text: Repli G

text: ArrayExpress

characteristic: broker name

text: common myeloid progenitor

text: diagnosis

characteristic: clinical history

text: acute myeloid leukemia B phenotype

characteristic: clinical information

text: human

characteristic: date

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: FACS Aria

characteristic: protocol

characteristic: sample id

text: Homo sapiens

text: male

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-

text: Sample 418

characteristic: title


E-MTAB-12238:Sample 419

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12238:Sample 419

text: Repli G

characteristic: WGA

text: ArrayExpress

text: relapse

text: acute myeloid leukemia B phenotype

text: human

characteristic: common name

characteristic: description

text: adult

text: acute myeloid leukemia

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: blood

text: FACS Aria

text: Homo sapiens

text: male

characteristic: sex

characteristic: subclone

text: Sample 419

text: 1:10 human CD45 positive out of mouse bone marrow 24

characteristic: xenograft


E-MTAB-12238:Sample 42

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12238:Sample 42

characteristic: Submitter Id

text: Repli G

text: ArrayExpress

characteristic: broker name

text: common myeloid progenitor

text: diagnosis

characteristic: clinical history

text: acute myeloid leukemia B phenotype

characteristic: clinical information

text: human

characteristic: date

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: immunophenotype

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone marrow

characteristic: organism part

text: FACS Aria - H4100 colony

text: Homo sapiens

text: male

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-

characteristic: time

text: Sample 42


E-MTAB-12238:Sample 420

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12238:Sample 420

text: Repli G

characteristic: WGA

text: ArrayExpress

text: relapse

text: acute myeloid leukemia B phenotype

text: human

characteristic: common name

characteristic: description

text: adult

text: acute myeloid leukemia

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: blood

text: FACS Aria

characteristic: protocol

characteristic: sample id

text: Homo sapiens

text: male

characteristic: sex

text: Sample 420

characteristic: title


E-MTAB-12238:Sample 421

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12238:Sample 421

characteristic: Submitter Id

text: Repli G

text: ArrayExpress

characteristic: broker name

text: myeloid cell

text: relapse

characteristic: clinical history

text: acute myeloid leukemia B phenotype

characteristic: clinical information

text: human

characteristic: date

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone marrow

text: FACS Aria

text: Homo sapiens

text: male

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-

characteristic: subclone

text: Sample 421


E-MTAB-12238:Sample 422

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12238:Sample 422

text: Repli G

characteristic: WGA

text: ArrayExpress

text: myeloid cell

text: relapse

text: acute myeloid leukemia B phenotype

text: human

characteristic: common name

characteristic: description

text: adult

text: acute myeloid leukemia

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: bone marrow

characteristic: organism part

text: FACS Aria

text: Homo sapiens

text: male

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-

characteristic: time

text: Sample 422


E-MTAB-12238:Sample 423

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12238:Sample 423

characteristic: Submitter Id

text: Repli G

text: ArrayExpress

characteristic: broker name

text: diagnosis

characteristic: clinical history

text: acute myeloid leukemia

characteristic: clinical information

text: human

characteristic: date

text: adult

text: acute myeloid leukemia

text: Homo sapiens

text: Homo sapiens

text: blood

text: FACS Aria

characteristic: protocol

characteristic: sample id

text: Homo sapiens

text: male

characteristic: sex

text: NPM1+ FLT3-ITD+; CD45 positive

text: Sample 423

characteristic: title

text: human CD45 positive out of mouse bone marrow 75

characteristic: xenograft


E-MTAB-12238:Sample 424

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12238:Sample 424

text: Repli G

characteristic: WGA

text: ArrayExpress

text: diagnosis

text: acute myeloid leukemia

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: FACS Aria

text: Homo sapiens

text: male

text: NPM1+ FLT3-ITD+; CD45 positive

characteristic: subclone

text: Sample 424


E-MTAB-12238:Sample 425

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12238:Sample 425

characteristic: Submitter Id

text: Repli G

text: ArrayExpress

characteristic: broker name

text: granulocyte monocyte progenitor cell

text: diagnosis

characteristic: clinical history

text: acute myeloid leukemia

characteristic: clinical information

text: human

characteristic: date

text: adult

text: acute myeloid leukemia

characteristic: disease

characteristic: immunophenotype

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: FACS Aria

characteristic: protocol

characteristic: sample id

text: Homo sapiens

text: male

text: NPM1+ FLT3-ITD+

characteristic: time

text: Sample 425

text: 1:10 human CD45 positive out of mouse bone marrow 75


E-MTAB-12238:Sample 426

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12238:Sample 426

text: Repli G

characteristic: WGA

text: ArrayExpress

text: granulocyte monocyte progenitor cell

text: diagnosis

text: acute myeloid leukemia

text: human

characteristic: common name

text: Protocols: CD34+ cells were isolated from PB or BM (following mononuclear cell separation) of AML patients by positive selection using anti-human CD34 microbeads. Enriched CD34+ cells were sorted by FACSariaII (BD bioscience, CA, USA) into four subpopulations of HSPCs according to their surface markers and CD33 expression. The sorted fractions were collected either into Iscove's modified Dulbecco's medium (IMDM) +20% fetal bovine serum (FBS) (Biological Industries #02-023-1A) to be further used in the colony forming unit (CFU) assay or into PBS+2%FBS to be used in the xenotransplantation assay. The CFU assay was adjusted to the generation of single cell-derived subclones. HSPCs were seeded in 1% standard methylcellulose medium supplemented with 37% FBS, 1.2% bovine serum albumin (BSA), 1% L-glutamine, 10-6M b-mercaptoethanol, 1 IU/ml of human erythropoietin (EPO), 50 ng/ml of human stem cell factor (SCF), 25 ng/ml of human FLT3 ligand, 10 ng/ml of interleukin 3 (IL-3), 10 ng/ml of interleukin 6 (IL-6), 10 ng/ml of granulocytecolony stimulating factor (G-CSF), 5 ng/ml of granulocyte-macrophage colony-stimulating factor (GM-CSF), 10 ng/ml of human thrombopoietin (TPO), 100 IU ml penicillin and 100 mg/ml streptomycin. Colonies were counted after 14 days and each of them was picked under sterile conditions. Every individual colony was divided into two cell suspensions to perform both genotyping analysis and xenotransplantation into NSG mice. xenograft protocol: NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ (NSG) mice (The Jackson Laboratory, Bar Harbor, Maine, USA) were maintained and bred under specific pathogen-free conditions at the Biomedical Core Facility (Faculty of Medicine, the Technion, Haifa, Israel). Twenty-four hours prior to transplantation, 8-12-week-old female NSG mice were sub-lethally irradiated with 225 cGy. Primary human cells were intra-femorally injected. The total number of cells transplanted per mouse depended on the number of viable cells obtained from the BM/PB of a patient [ranged from 1 colony (a single cell-derived subclone) to 106 cells]. The animals were sacrificed 8-30 weeks after transplantation or if tumors developed in the injected knee. The BM was then harvested. Human engraftment was evaluated by flow cytometry using the following anti-human specific antibodies: anti-CD45-APC Cyanine7 (APC-Cy7) (BioLegend #304014 clone H130); anti-CD33-BV510 (BioLegend #366610); anti-CD34-BV421 (BioLegend #343610); anti-CD38-FITC (BD #555459); anti-CD15 APC (BD #551376); anti-CD19 PE-CY7 (BD #557835); Cell viability was obtained using Propidium Iodide - PI (BioLegend #421301). Analyses were performed using FlowJo software v.10 (Treestar, OR, USA), and the expression of markers was assessed and presented as the percentage of stained cells. The threshold for engraftment detection was 0.1% of human CD45+ cells. All flow cytometry analyses were done using an LSR II (BD Bioscience, CA, USA) or FACSariaII (BD Bioscience, CA, USA) device. Engraftment of >5% of hCD45+ cells with the major CD33+ population (>60% of the hCD45+ cells) was classified as overt leukemia; the presence of 0.1-5% of hCD45+ cells or the presence of >5% of hCD45+ cells with <60% of the CD33+ population in the hCD45+ cells was classified as non-overt leukemia; and the presence of <0.1% of human CD45+ (hCD45+) population was considered as non-engraftment. hCD45+ cells were sorted and underwent whole genome amplification (WGA) for further genotyping assays. CD34+ cells were isolated from PB or BM (following mononuclear cell separation) of AML patients by positive selection using anti-human CD34 microbeads. Enriched CD34+ cells were sorted by FACSariaII (BD bioscience, CA, USA) into four subpopulations of HSPCs according to their surface markers and CD33 expression. The sorted fractions were collected either into Iscove's modified Dulbecco's medium (IMDM) +20% fetal bovine serum (FBS) (Biological Industries #02-023-1A) to be further used in the colony forming unit (CFU) assay or into PBS+2%FBS to be used in the xenotransplantation assay. The CFU assay was adjusted to the generation of single cell-derived subclones. HSPCs were seeded in 1% standard methylcellulose medium supplemented with 37% FBS, 1.2% bovine serum albumin (BSA), 1% L-glutamine, 10-6M b-mercaptoethanol, 1 IU/ml of human erythropoietin (EPO), 50 ng/ml of human stem cell factor (SCF), 25 ng/ml of human FLT3 ligand, 10 ng/ml of interleukin 3 (IL-3), 10 ng/ml of interleukin 6 (IL-6), 10 ng/ml of granulocytecolony stimulating factor (G-CSF), 5 ng/ml of granulocyte-macrophage colony-stimulating factor (GM-CSF), 10 ng/ml of human thrombopoietin (TPO), 100 IU ml penicillin and 100 mg/ml streptomycin. Colonies were counted after 14 days and each of them was picked under sterile conditions. Every individual colony was divided into two cell suspensions to perform both genotyping analysis and xenotransplantation into NSG mice One µl of DNA template was added to a hybridization mix together with an MIP pool (final concentration of 0.05pM per probe) in 1x Ampligase buffer (Epicentre). The mix was incubated in a thermal cycler according to the following program: 98°C for 3 minutes, 85°C for 30 minutes, 60°C for 60 minutes and 56°C for 1 or 2 overnight incubations. The product was mixed with (final concentration in brackets): dNTPs (Larova, 15pM), Betaine (375 mM, Sigma-Aldrich,), NAD+ (1 mM, New England Biolabs), additional Ampligase buffer (0.5x), Ampligase (total of 1.25U, Epicentre) and Phusion HF (0.16U, New England Biolabs). The mix was incubated at 56°C for 60 minutes followed by 72°C for 20 minutes. Enzymatic digestion of linear probes was performed by adding Exonuclease I (4U, New England Biolabs) and Exonuclease III (25U, New England Biolabs). The mix was incubated at 37°C for 2 hours, followed by 80°C for 20 minutes. The final product was amplified using iProof HF Master Mix (Biorad). Samples were pooled and concentrated using AMPure XP beads (Beckman Coulter) at 1.3x volumetric concentration, size-selected (190-370bp) using Blue Pippin (Sage scientific), and sequenced in either NextSeq or Novaseq6000 (Illumina) 2X151bp paired-end run using custom primers as described in the past(Biezuner et al., 2022)

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text: NPM1+ FLT3-ITD+

text: Sample 426

characteristic: title

characteristic: xenograft


E-MTAB-12238:Sample 427

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E-MTAB-12238:Sample 428

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E-MTAB-12238:Sample 429

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text: human CD45 positive out of mouse bone marrow 90

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E-MTAB-12238:Sample 43

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text: Department of Molecular Cell Biology, Weizmann Institute of Science

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E-MTAB-12238:Sample 430

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E-MTAB-12238:Sample 431

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E-MTAB-12238:Sample 432

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E-MTAB-12238:Sample 433

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text: 1:10 human CD45 positive out of mouse bone marrow 90

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E-MTAB-12238:Sample 434

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text: Sample 434


E-MTAB-12238:Sample 435

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text: Sample 435


E-MTAB-12238:Sample 436

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text: adult

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text: FACS Aria

text: Homo sapiens

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text: Sample 436

characteristic: title


E-MTAB-12238:Sample 437

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text: Homo sapiens

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text: Sample 437


E-MTAB-12238:Sample 438

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text: E-MTAB-12238:Sample 438

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characteristic: sex

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-

characteristic: subclone

characteristic: time

text: Sample 438


E-MTAB-12238:Sample 439

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text: adult

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text: acute myeloid leukemia

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text: Homo sapiens

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text: FACS Aria

text: Homo sapiens

text: male

text: NPM1+ FLT3-ITD+; CD45 positive

text: Sample 439

characteristic: title

text: human CD45 positive out of mouse bone marrow 76

characteristic: xenograft


E-MTAB-12238:Sample 44

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text: E-MTAB-12238:Sample 44

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text: human

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text: Homo sapiens

characteristic: organism

text: Homo sapiens

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text: FACS Aria

characteristic: protocol

characteristic: sample id

text: Homo sapiens

text: male

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-

text: Sample 44


E-MTAB-12238:Sample 440

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text: E-MTAB-12238:Sample 440

text: Repli G

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text: acute myeloid leukemia

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characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: blood

text: FACS Aria

text: Homo sapiens

text: male

characteristic: sex

text: NPM1+ FLT3-ITD+; CD45 positive

characteristic: subclone

characteristic: time

text: Sample 440

characteristic: title


E-MTAB-12238:Sample 441

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text: public

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text: E-MTAB-12238:Sample 441

characteristic: Submitter Id

text: Repli G

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characteristic: broker name

text: common lymphoid progenitor

text: diagnosis

characteristic: clinical history

text: acute myeloid leukemia

characteristic: clinical information

text: human

characteristic: date

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text: CD34+, CD38-,CD90+/-, CD45Ra+

characteristic: immunophenotype

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

characteristic: organism part

text: FACS Aria

characteristic: protocol

text: Homo sapiens

text: male

text: NPM1+ FLT3-ITD+

text: Sample 441

text: 1:10 human CD45 positive out of mouse bone marrow 76

characteristic: xenograft


E-MTAB-12238:Sample 442

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text: public

text: E-MTAB-12238:Sample 442

text: Repli G

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text: acute myeloid leukemia

text: human

characteristic: common name

characteristic: description

text: adult

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text: acute myeloid leukemia

characteristic: disease

text: CD34+, CD38-,CD90+/-, CD45Ra+

text: Homo sapiens

text: Homo sapiens

text: blood

text: FACS Aria

characteristic: sample id

text: Homo sapiens

text: male

characteristic: sex

text: NPM1+ FLT3-ITD+

characteristic: subclone

text: Sample 442


E-MTAB-12238:Sample 443

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text: public

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characteristic: SRA accession

text: E-MTAB-12238:Sample 443

characteristic: Submitter Id

text: Repli G

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characteristic: broker name

text: relapse

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text: acute myeloid leukemia B phenotype

characteristic: clinical information

text: human

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text: adult

text: acute myeloid leukemia

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone marrow

characteristic: organism part

text: Miltenyi column -CD34+ Enrichment by magnetic beads

text: Homo sapiens

text: male

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-; CD34 positive ; CD34 positive

characteristic: time

text: Sample 443

characteristic: title


E-MTAB-12238:Sample 444

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text: acute myeloid leukemia B phenotype

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characteristic: common name

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text: acute myeloid leukemia

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text: Homo sapiens

text: Homo sapiens

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text: Homo sapiens

text: male

text: Sample 444


E-MTAB-12238:Sample 445

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text: E-MTAB-12238:Sample 445

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text: Repli G

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text: diagnosis

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text: human

characteristic: date

text: adult

text: acute myeloid leukemia

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text: Homo sapiens

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text: FACS Aria

characteristic: sample id

text: Homo sapiens

text: male

characteristic: sex

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text: Sample 445

text: human CD45 positive out of mouse bone marrow 91

characteristic: xenograft


E-MTAB-12238:Sample 446

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text: Homo sapiens

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text: FACS Aria

text: Homo sapiens

text: male

characteristic: time

text: Sample 446

characteristic: title


E-MTAB-12238:Sample 447

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text: E-MTAB-12238:Sample 447

characteristic: Submitter Id

text: Repli G

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text: relapse

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text: acute myeloid leukemia B phenotype

characteristic: clinical information

text: human

characteristic: date

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characteristic: developmental stage

text: acute myeloid leukemia

characteristic: disease

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: bone marrow

characteristic: protocol

characteristic: sample id

text: Homo sapiens

text: male

text: Sample 447