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Sample GSM7170182 Query DataSets for GSM7170182
Status Public on Feb 12, 2024
Title cord-blood CD34+ cells, MPC-FKBP12-nHA-UBTF-TD, dTAG-13-1µM, KMT2A, rep2
Sample type SRA
 
Source name Human cord-blood CD34+ cells
Organism Homo sapiens
Characteristics expression vector: MPC-FKBP12-nHA-UBTF-TD
treatment: dTAG-13, 1µM
cell type: Human cord-blood CD34+ cells
chip antibody: KMT2A (Bethyl Laboratories, A300-086A)
Growth protocol Cells were growin in SFEM II supplemented with pen-strep, I-glutamine, and recombinant human SCF, FLT-3, TPO and IL-6 (all 50ng/mL PeproTech), UM729 (#72332, STEMCELL Technologies) and SR-1 (1µmol/L, #72344, STEMCELL Technologies)
Extracted molecule genomic DNA
Extraction protocol CUT&RUN was performed following the kit from EpiCypher (cat# 14-1048)
CUT&RUN DNA libraries were made following NEBNext Ultra II DNA Library Prep Kit for Illumina (cat# E7103), PCR amplification was done for 12 cycles
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description Figure 3D-E, Supplemental Figure 3O-P
Data processing To obtain quality reads, raw reads were processed and trimmed with Trim_galore (v0.4.4) from cutadapt (DOI: 10.14806ej.17.1.200) and FASTQC analysis. A default quality score cutoff of Q20 is used. Quality trimmed reads were then mapped to "hg38+rDNA” (DOI: 10.1101/2022.11.10.514243) genome build by bwa (v0.7.12-r1039) and converted to a bam file by samtools (v1.2).
Duplicate reads were marked with biobambam2 (v2.0.87, DOI: 10.1186/175109473-9-13). Uniquely mapped and properly paired reads were then extracted with samtools (v1.2, "-F 1804 -q 1") and sorted by read name using biobambam2 (v2.0.87)
bedtools(v2.17.0, PMID: 20110278) were used to convert bam file to bedpe file as fragments. Fragments with size shorter than 2000bp were extracted and center 80bp of each fragment were used to generate bigwig track files by UCSC tools (v4) and visualized using IGV (v2.16.0).
Narrow peaks were called with MACS2 (v2.1.1.20160309, parameters "-q 0.05") and broad peaks were called by SICER (v1.1, parameters "hg38 1 200 fragmentsize 0.86 600 0.00001").
To perform statistical test between experimental groups (DMSO/dTAG), fragments for each reference peak were counted with intersect command from pybedtools (v0.9.1). Next, the number of raw reads mapping per peak were converted to FPKM unit (Fragments Per Kilo base per Million mapped reads), and TMM (trimmed mean of M-values) from edgeR package. Next, we used limma-voom approach to assess the significance of differential peak binding. Significant peaks were defined by log2FC < -1 or > 1 and FDR < 0.05.
Assembly: hg38+ custom rDNA build from DOI: https://doi.org/10.1101/2022.11.10.514243
Supplementary files format and content: bw
Library strategy: CUT&RUN
 
Submission date Apr 13, 2023
Last update date Feb 12, 2024
Contact name Guangchun Song
Phone 901-595-5722
Organization name St Jude Children's Research Hospital
Department Pathology
Lab Klco
Street address 262 Danny Thomas Place
City Memphis
State/province TN
ZIP/Postal code 38105
Country USA
 
Platform ID GPL24676
Series (2)
GSE229664 UBTF tandem duplication acute myeloid leukemias are sensitive to menin inhibition [Cut&Run]
GSE229666 UBTF tandem duplication acute myeloid leukemias are sensitive to menin inhibition
Relations
BioSample SAMN34172531
SRA SRX19960136

Supplementary file Size Download File type/resource
GSM7170182_2414951_SJNORM077216_C9-CD34_5E_FKBP12-TD54_1uM_dTag_rep2-KMT2A-AB2.CRall.bw 158.9 Mb (ftp)(http) BW
GSM7170182_2414951_SJNORM077216_C9-CD34_5E_FKBP12-TD54_1uM_dTag_rep2-KMT2A-AB2.b150bp.bw 158.9 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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