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Status |
Public on Mar 01, 2023 |
Title |
Kasumi-1_SMARCA5-FKBP12_6hdTAG_antiCTCF_1 [CUT&RUN] |
Sample type |
SRA |
|
|
Source name |
Kasumi-1 SMARCA5-FKBP12-1xFLAG cells
|
Organism |
Homo sapiens |
Characteristics |
cell line: Kasumi-1 genotype/variation: SMARCA5-FKBP12F36V-1xFLAG treatment: dTAG47 time point: 6hr assay: Cut&Run antibody: anti-CTCF (Millipore, 07-729) secondary antibody: anti-rabbit (Invitrogen, 31238)
|
Treatment protocol |
Cells were treated with 500 nM dTAG-47 for the indicated timepoints.
|
Growth protocol |
Kasumi-1 cells were grown in RPMI +20% FBS +50 U/ml penicillin, 50 μg/ml streptomycin, and 2mM L-glutamine.
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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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Description |
5176-MB-5 6hr_500nM_dTAG47
|
Data processing |
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 ((anti-flag: narrowPeak, q=0.05),(anti-CTCF: narrowPeak, q=0.001)). For anti-flag cut&run +/-dTAG, differential peaks were identified by Diffbind/DESeq2 using yeast spike-in for normalization. Genome_build: hg19 (GRCh37) Supplementary_files_format_and_content: bigwig files were generated using deepTools. Supplementary_files_format_and_content: narrowPeak files. Supplementary_files_format_and_content: 070220_cutandrun_S5_peakinfo_qv0.05.csv: Peak information; comma-separate values. Supplementary_files_format_and_content: 070220_S5_cutandrun_DESEQ_qv0.05.csv: Differential peaks; comma-separate values.
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Submission date |
Oct 29, 2020 |
Last update date |
Mar 01, 2023 |
Contact name |
Scott W Hiebert |
E-mail(s) |
mbomber92@gmail.com, scott.hiebert@vanderbilt.edu
|
Organization name |
Vanderbilt University
|
Department |
Biochemistry
|
Lab |
Dr. Scott Hiebert
|
Street address |
512 B Preston Research Building
|
City |
Nashville |
State/province |
TN |
ZIP/Postal code |
37232 |
Country |
USA |
|
|
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 |
|
Relations |
BioSample |
SAMN16597950 |
SRA |
SRX9402767 |