|
| Status |
Public on Mar 01, 2023 |
| Title |
Kasumi-1_SMARCA5FKBP12_G1_6hdTAG47_2 [ATAC-Seq] |
| Sample type |
SRA |
| |
|
| Source name |
Kasumi-1 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Kasumi-1 cells
treatment: 6hr_500nM_dTAG47
time: Synchronized cells_G1
|
| 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. OCI-LY1 cells were grown in IMDM +10% FetalPlex +50 U/ml penicillin, 50 μg/ml streptomycin, and 2mM L-glutamine. HEL cells were grown in RPMI +10% FetalPlex +50 U/ml penicillin, 50 μg/ml streptomycin, and 2mM L-glutamine.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
followed ATAC-seq protocol, isolated nuclei
Libraries were constructed using the NEBNext Ultra II DNA Library Prep Kit or Active Motif Kit
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
7189-3-4.withdup.j.r.Eblacklist.q0.05.narrowPeak
7189-MB-4
|
| 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 Genrich (q 0.05 -j -r -E ; v. 0.6 )
for ATAC-seq +/-dTAG, differential peaks were identified by Diffbind/DESeq2, using 0h as a negative control
Assembly: hg19
Supplementary files format and content: Genrich peak files, differential peak files generated by Diffbind+DESeq2
|
| |
|
| Submission date |
Dec 07, 2022 |
| 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) |
| GSE160469 |
Human SMARCA5 Is Continuously Required to Maintain Nucleosome Spacing [ATAC-seq] |
| GSE160470 |
Human SMARCA5 Is Continuously Required to Maintain Nucleosome Spacing |
|
| Relations |
| BioSample |
SAMN32103932 |
| SRA |
SRX18534312 |
