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Status |
Public on Feb 12, 2024 |
Title |
cord-blood CD34+ cells, MPC-FKBP12-nHA-UBTF-TD, dTAG-13-1µM, KMT2A, rep2 |
Sample type |
SRA |
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Source name |
Human cord-blood CD34+ cells
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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)
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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)
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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
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Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina NovaSeq 6000 |
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Description |
Figure 3D-E, Supplemental Figure 3O-P
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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
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Submission date |
Apr 13, 2023 |
Last update date |
Feb 12, 2024 |
Contact name |
Guangchun Song |
Phone |
901-595-5722
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Organization name |
St Jude Children's Research Hospital
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Department |
Pathology
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Lab |
Klco
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Street address |
262 Danny Thomas Place
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City |
Memphis |
State/province |
TN |
ZIP/Postal code |
38105 |
Country |
USA |
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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 |
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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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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