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Status |
Public on Mar 01, 2023 |
Title |
HEL_SMARCA5-FKBP12(+)dTAG_antiFlag_1 [CUT&RUN] |
Sample type |
SRA |
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Source name |
HEL SMARCA5-FKBP12-1xFLAG cells
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Organism |
Homo sapiens |
Characteristics |
cell line: HEL SMARCA5-FKBP12-1xFLAG cells treatment: 18htreated_500nM_dTAG47 assay: CUT&RUN antibody: anti-flag (Sigma, F1804) secondary antibody: anti-mouse (abcam, ab46540)
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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 |
SAMN32168646 |
SRA |
SRX18648518 |
Supplementary file |
Size |
Download |
File type/resource |
GSM6813314_6965-MB-3.hg19.keepdupall.q0.001.BAMPE_peaks.BLfiltered.narrowPeak.gz |
36.7 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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