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| Status |
Public on Mar 01, 2023 |
| Title |
Kasumi-1_SMARCA5-FKBP12_24hdTAG_antiETOZnf_1 [CUT&RUN] |
| Sample type |
SRA |
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| Source name |
Kasumi-1 SMARCA5-FKBP12-1xFLAG cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: Kasumi-1 SMARCA5-FKBP12-1xFLAG cells
treatment: 24hr_500nM_dTAG47
assay: CUT&RUN
antibody: anti-ETOZnf(in house)
secondary antibody: anti-rabbit (Invitrogen, 31238)
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| Treatment protocol |
cells were treated with 500 nM dTAG-47 for the indicated timepoints
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| Growth protocol |
Kasumi-1 cells were grown in RPMI +20% FBS +50 U/ml penicillin, 50 μg/ml streptomycin, and 2mM L-glutamine. CD34+ cells were cultured in IMDM + 20% FBS, 55 μM BME, 50 U/ml penicillin, 50 μg/ml streptomycin, 2mM L-glutamine, and 10 ng/mL SCF, Flt3-L, TPO, IL-3, and IL-6
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For Cut&Run anti-flag, released DNA fragments were extracted using phenol:chloroform:IAA and ethanol precipitation. For Cut&Run anti-CTCF, released DNA fragments were extracted using NEB Monarch Nucleic Acid Purification Kits.
Libraries were constructed using the NEBNext Ultra II DNA Library Prep Kit
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
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 (( anti-flag: narrowPeak, q=0.001),(anti-CTCF, anti-RUNX1, anti-ETOZnf, anti-H2AZ: narrowPeak, q=0.01), (anti-H3K27me3: broadPeak, q=0.01))
CUT&RUN +/-dTAG at indicated time points, differential peaks were identified by Diffbind/DESeq2 using total counts for normalization
Assembly: hg19
bigwig files were generated using deepTools
Supplementary files format and content: bigWigs, narrowPeak, broadPeaks, counts tables with differential analysis
Library strategy: Cut&Run
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| Submission date |
Dec 12, 2022 |
| Last update date |
Mar 03, 2023 |
| Contact name |
Scott W Hiebert |
| E-mail(s) |
mbomber92@gmail.com, scott.hiebert@vanderbilt.edu
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| Organization name |
Vanderbilt University
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| Department |
Biochemistry
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| Lab |
Dr. Scott Hiebert
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| Street address |
512 B Preston Research Building
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| City |
Nashville |
| State/province |
TN |
| ZIP/Postal code |
37232 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE160468 |
Human SMARCA5 Is Continuously Required to Maintain Nucleosome Spacing [CUT&RUN] |
| GSE160470 |
Human SMARCA5 Is Continuously Required to Maintain Nucleosome Spacing |
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| Relations |
| BioSample |
SAMN32168634 |
| SRA |
SRX18648506 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6813302_5568-MB-11.ETOZnf.hg19.keepdupall.q0.01.BAMPE_peaks.BLfiltered.narrowPeak.gz |
732.6 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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