|
| Status |
Public on Mar 01, 2023 |
| Title |
Kasumi-1_SMARCA5-FKBP12_24hdTAG_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: 24hr
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.
|
| 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.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
5176-MB-7
24hr_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.
|
| |
|
| 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 |
SAMN16597948 |
| SRA |
SRX9402769 |
