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| Status |
Public on Mar 01, 2023 |
| Title |
Kasumi-1_SMARCA5FKBP12_0hdTAG47_2 [ATAC-seq] |
| Sample type |
SRA |
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| Source name |
Kasumi-1 cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: Kasumi-1
genotype/variation: SMARCA5-FKBP12F36V
treatment: Untreated
time point: 0hr
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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 |
Followed ATAC-seq protocol, isolated nuclei.
Libraries were constructed using the NEBNext Ultra II DNA Library Prep Kit.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Adaptor trimming with Trimmomatic-0.32 PE ILLUMINACLIP:atac_adaptor.txt:2:30:7 MINLEN:15
Alignment to hg19+dm3 genome with bowtie2.
High quality reads (F4q10) were filtered using samtools.
Peaks called with MACS2 (narrowPeak, q=0.01).
For ATAC-seq +/-dTAG, differential peaks were identified by Diffbind/DESeq2 using S2 Drosophila spike-in for normalization, using 0h as a negative control.
bigwig files were generated using deepTools.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigwig, MACS2 peak files, differential peak files generated by Diffbind+DESeq2.
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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
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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) |
| GSE160469 |
Human SMARCA5 Is Continuously Required to Maintain Nucleosome Spacing [ATAC-seq] |
| GSE160470 |
Human SMARCA5 Is Continuously Required to Maintain Nucleosome Spacing |
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| Relations |
| BioSample |
SAMN16597965 |
| SRA |
SRX9402794 |
| Supplementary data files not provided |
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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