|
Status |
Public on Mar 01, 2023 |
Title |
Kasumi-1_SMARCA5FKBP12_6hdTAG47_1 [Mnase-Seq] |
Sample type |
SRA |
|
|
Source name |
Kasumi-1 cells
|
Organism |
Homo sapiens |
Characteristics |
cell line: Kasumi-1 cells treatment: 6hr_500nM_dTAG47
|
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. 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
|
Extracted molecule |
genomic DNA |
Extraction protocol |
followed MNase-seq protocol, isolated nuclei Libraries were constructed using the NEBNext Ultra II DNA Library Prep Kit
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|
|
Library strategy |
MNase-Seq |
Library source |
genomic |
Library selection |
MNase |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Data processing |
Adaptor trimming with Trimmomatic-0.32 PE ILLUMINACLIP:atac_adaptor.txt:2:30:7 MINLEN:15 alignment to hg19 genome with bowtie2 high quality reads (F4q10) were filtered using samtools motifs from CTCF CUT&RUN deteremined by fimo bam files were fltered with deepTools alignmentsieve bigWig files around CTCF motifs with deepTools --MNase --minFragmentLength 130 --maxFragmentLength 210 --normalization CPM Assembly: hg19 Supplementary files format and content: bigwig
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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
|
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) |
GSE160470 |
Human SMARCA5 Is Continuously Required to Maintain Nucleosome Spacing |
GSE220778 |
Human SMARCA5 Is Continuously Required to Maintain Nucleosome Spacing [MNAse-Seq] |
|
Relations |
BioSample |
SAMN32175403 |
SRA |
SRX18654967 |