GSE153279

GSE GEO

View on GEO Export SRA CSV

Definition of a Small Core Transcriptional Circuit Regulated by AML1-ETO [ChIP-seq, Cut&Run]

Organism: Homo sapiens

Platform: GPL24676

Samples: 9

Experiment Types:

Genome binding/occupancy profiling by high throughput sequencing

Submitted: Jun 25 2020

Last Updated: Apr 01 2021

Status: Public on Dec 31 2020

Contact: Scott,,Hiebert (Vanderbilt University)

Relations

SubSeries of: GSE153281 BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA641910 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP268847

Summary

Transcription factors regulate gene networks controlling normal hematopoiesis and are frequently deregulated in acute myeloid leukemia (AML). Critical to our understanding of the mechanism of cellular transformation by oncogenic transcription factors is the ability to define their direct gene targets. However, gene network cascades can change within minutes to hours, making it difficult to distinguish direct from secondary or compensatory transcriptional changes by traditional methodologies. Utilizing CRISPR-based genome editing, we inserted a degron tag into the endogenous AML1-ETO locus of Kasumi-1 cells, as well as overexpressed a degradable AML1-ETO protein in CD34+ human cord blood cells. This allowed rapid AML1-ETO protein degradation upon addition of a proteolysis targeting chimera (PROTAC). Furthermore, by combining rapid degradation with nascent transcript analysis (PRO-seq), RNA-seq and Cut&Run, we have defined the core AML1-ETO regulatory network. De-repression of this small set of genes set off a cascade of transcriptional events resulting in myeloid differentiation.

Overall Design

Cut&Run was performed to define genome-wide binding of AML1-ETO-FKBP12F36V-2xHA in both Kasumi-1 cells and CD34+ cord blood cultures. Cut&Run using anti-ETO confirmed that the FKBP-2xHA tag had not altered AML1-ETO binding. ChIP-seq for H3K27ac was performed before and after 24 hr dTAG treatment.

Analysis (13 steps)

View Data Processing

Processing steps for GSE153279

Library strategy: Cut&Run
For Cut&Run:
Adaptor trimming with Trimmomatic-0.32.
Alignment to hg19+scer genome with bowtie2.
High quality reads (F4q10) were filtered using samtools.
Peaks called with MACS2 (narrowPeak, q=0.001).
For HA Cut&Run +/-dTAG, differential peaks were identified by Diffbind/DESeq2 using yeast spike-in for normalization.
bigWig files were generated using deepTools and bedGraph files were generated using Homer.

Showing first 8 steps.

Supplementary Files (5)

GSE153279_042420_HA-AE_cutandrun_diffbind-deseq2_q0.001.csv.gz Download

GSE153279_042420_HA_AE_Diffbind-peakinfo_q0.001.csv.gz Download

GSE153279_CD34_HA_merged_noNeg_nomodel_extsize300_q0.001_peaks.txt.gz Download

GSE153279_New_ZnF_q0.001_peaks.txt.gz Download

GSE153279_RAW.tar Download

GEO Samples (9)

GSM4637309 GSM4637310 GSM4637311 GSM4637312 GSM4637313 GSM4637314 GSM4637315 GSM4637316 GSM4637317

Dataset Citations (1)

PubMed citation (PMID 33382982)

SRA Experiments (9) and Runs (9)

Total: 37066 MB

SRX8617898 SRP268847 OTHER PAIRED

GSM4637312: Kasumi-1_(+)dTAG_anti-HA-2 [Cut&Run]; Homo sapiens; OTHER

Sample: SRS6906942

BioProject: PRJNA641910

BioSample: SAMN15369725

Platform: ILLUMINA

Instrument: Illumina NovaSeq 6000

Organism: Homo sapiens

Sample attributes

source_name: Kasumi-1_AE-FKBP-2xHA_cells

cell line: Kasumi-1

genotype variation: AML1-ETO-FKBP12F36V-2xHA

treatment: dTAG

antibody: anti-HA

Original files (1)

Kasumi-1_AE-FKBP-2xHA_cells

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR12092008	28706021	8611806300	2576.41	4617-MB-4_S74_L005_R1_001.fastq.gz, 4617-MB-4_S74_L005_R2_001.fastq.g…	SRA

SRX8617899 SRP268847 OTHER PAIRED

GSM4637313: Kasumi-1_parental_anti-ETO [Cut&Run]; Homo sapiens; OTHER

Sample: SRS6906943

BioProject: PRJNA641910

BioSample: SAMN15369724

Platform: ILLUMINA

Instrument: Illumina NovaSeq 6000

Organism: Homo sapiens

Sample attributes

source_name: Kasumi-1_parental cells

cell line: Kasumi-1

genotype variation: Parental

antibody: anti-ETO

Original files (1)

Kasumi-1_parental cells

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR12092009	14600130	4367734551	1443.42	3856-CS-34-CCAAGGTT-AGGATAGC_S286_R1_001.fastq.gz, 3856-CS-34-CCAAGGT…	SRA

SRX8617900 SRP268847 ChIP-Seq PAIRED

GSM4637314: Kasumi-1_(-)dTAG_anti-H3K27ac [ChIP-seq]; Homo sapiens; ChIP-Seq

Sample: SRS6906944

BioProject: PRJNA641910

BioSample: SAMN15369723

Platform: ILLUMINA

Instrument: Illumina NovaSeq 6000

Organism: Homo sapiens

Sample attributes

source_name: Kasumi-1_AE-FKBP-2xHA_cells

cell line: Kasumi-1

genotype variation: AML1-ETO-FKBP12F36V-2xHA

treatment: No dTAG

antibody: anti-H3K27ac

Original files (1)

Kasumi-1_AE-FKBP-2xHA_cells

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR12092010	87756058	26245725897	8286.55	3691-CS-1-TTACCGAC-CGAATACG_S1_R1_001.fastq.gz, 3691-CS-1-TTACCGAC-CG…	SRA

SRX8617901 SRP268847 ChIP-Seq PAIRED

GSM4637315: Kasumi-1_(+)dTAG_anti-H3K27ac [ChIP-seq]; Homo sapiens; ChIP-Seq

Sample: SRS6906945

BioProject: PRJNA641910

BioSample: SAMN15369719

Platform: ILLUMINA

Instrument: Illumina NovaSeq 6000

Organism: Homo sapiens

Sample attributes

source_name: Kasumi-1_AE-FKBP-2xHA_cells

cell line: Kasumi-1

genotype variation: AML1-ETO-FKBP12F36V-2xHA

treatment: dTAG

antibody: anti-H3K27ac

Original files (1)

Kasumi-1_AE-FKBP-2xHA_cells

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR12092011	109822327	32845740280	10503.2	3691-CS-7-TAGGAGCT-GCCTTAAC_S5_R1_001.fastq.gz, 3691-CS-7-TAGGAGCT-GC…	SRA

SRX8617902 SRP268847 OTHER PAIRED

GSM4637316: CD34+_anti-HA-1 [Cut&Run]; Homo sapiens; OTHER

Sample: SRS6906946

BioProject: PRJNA641910

BioSample: SAMN15369718

Platform: ILLUMINA

Instrument: Illumina NovaSeq 6000

Organism: Homo sapiens

Sample attributes

source_name: CD34+_human_cord_blood-AE-FKBP-2xHA

cell type: CD34+ cord blood cells

genotype variation: AML1-ETO-FKBP12F36V-2xHA

antibody: anti-HA

Original files (1)

CD34+_human_cord_blood-AE-FKBP-2xHA

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR12092012	25652764	7695829200	2722.86	4699-KS-3_S3_L005_R1_001.fastq.gz, 4699-KS-3_S3_L005_R2_001.fastq.gz,…	SRA

SRX8617903 SRP268847 OTHER PAIRED

GSM4637317: CD34+_anti-HA-2 [Cut&Run]; Homo sapiens; OTHER

Sample: SRS6906947

BioProject: PRJNA641910

BioSample: SAMN15369717

Platform: ILLUMINA

Instrument: Illumina NovaSeq 6000

Organism: Homo sapiens

Sample attributes

source_name: CD34+_human_cord_blood-AE-FKBP-2xHA

cell type: CD34+ cord blood cells

genotype variation: AML1-ETO-FKBP12F36V-2xHA

antibody: anti-HA

Original files (1)

CD34+_human_cord_blood-AE-FKBP-2xHA

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR12092013	24716267	7414880100	2517.72	4699-KS-4_S4_L005_R1_001.fastq.gz, 4699-KS-4_S4_L005_R2_001.fastq.gz,…	SRA

SRX8617904 SRP268847 OTHER PAIRED

GSM4637309: Kasumi-1_(-)dTAG_anti-HA-1 [Cut&Run]; Homo sapiens; OTHER

Sample: SRS6906948

BioProject: PRJNA641910

BioSample: SAMN15369722

Platform: ILLUMINA

Instrument: Illumina NovaSeq 6000

Organism: Homo sapiens

Sample attributes

source_name: Kasumi-1_AE-FKBP-2xHA_cells

cell line: Kasumi-1

genotype variation: AML1-ETO-FKBP12F36V-2xHA

treatment: No dTAG

antibody: anti-HA

Original files (1)

Kasumi-1_AE-FKBP-2xHA_cells

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR12092005	28556017	8566805100	2612.06	4617-MB-1_S71_L005_R1_001.fastq.gz, 4617-MB-1_S71_L005_R2_001.fastq.g…	SRA

SRX8617905 SRP268847 OTHER PAIRED

GSM4637310: Kasumi-1_(-)dTAG_anti-HA-2 [Cut&Run]; Homo sapiens; OTHER

Sample: SRS6906949

BioProject: PRJNA641910

BioSample: SAMN15369721

Platform: ILLUMINA

Instrument: Illumina NovaSeq 6000

Organism: Homo sapiens

Sample attributes

source_name: Kasumi-1_AE-FKBP-2xHA_cells

cell line: Kasumi-1

genotype variation: AML1-ETO-FKBP12F36V-2xHA

treatment: No dTAG

antibody: anti-HA

Original files (1)

Kasumi-1_AE-FKBP-2xHA_cells

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR12092006	30942995	9282898500	2830.41	4617-MB-2_S72_L005_R1_001.fastq.gz, 4617-MB-2_S72_L005_R2_001.fastq.g…	SRA

SRX8617906 SRP268847 OTHER PAIRED

GSM4637311: Kasumi-1_(+)dTAG_anti-HA-1 [Cut&Run]; Homo sapiens; OTHER

Sample: SRS6906950

BioProject: PRJNA641910

BioSample: SAMN15369720

Platform: ILLUMINA

Instrument: Illumina NovaSeq 6000

Organism: Homo sapiens

Sample attributes

source_name: Kasumi-1_AE-FKBP-2xHA_cells

cell line: Kasumi-1

genotype variation: AML1-ETO-FKBP12F36V-2xHA

treatment: dTAG

antibody: anti-HA

Original files (1)

Kasumi-1_AE-FKBP-2xHA_cells

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR12092007	38793958	11638187400	3572.94	4617-MB-3_S73_L005_R1_001.fastq.gz, 4617-MB-3_S73_L005_R2_001.fastq.g…	SRA

Linked Publications (1)

Identification of the global miR-130a targetome reveals a role for TBL1XR1 in hematopoietic stem cell self-renewal and t(8;21) AML.

Cell reports · 2022

Data Files (9)

Accession	File Name	Stored Type	Size	Download
—	3691-CS-1-TTACCGAC-CGAATACG_S1_R1_001.fastq.gz	ChIP-Seq	8.1 GB	link
—	3691-CS-7-TAGGAGCT-GCCTTAAC_S5_R1_001.fastq.gz	ChIP-Seq	10.3 GB	link
—	3856-CS-34-CCAAGGTT-AGGATAGC_S286_R1_001.fastq.gz	OTHER	1.4 GB	link
—	4617-MB-1_S71_L005_R1_001.fastq.gz	OTHER	2.6 GB	link
—	4617-MB-2_S72_L005_R1_001.fastq.gz	OTHER	2.8 GB	link
—	4617-MB-3_S73_L005_R1_001.fastq.gz	OTHER	3.5 GB	link
—	4617-MB-4_S74_L005_R1_001.fastq.gz	OTHER	2.5 GB	link
—	4699-KS-3_S3_L005_R1_001.fastq.gz	OTHER	2.7 GB	link
—	4699-KS-4_S4_L005_R1_001.fastq.gz	OTHER	2.5 GB	link