|
Status |
Public on Mar 01, 2023 |
Title |
HEL_SMARCA5FKBP12_0hdTAG47_2 [ATAC-Seq] |
Sample type |
SRA |
|
|
Source name |
HEL cells
|
Organism |
Homo sapiens |
Characteristics |
cell line: HEL cells treatment: untreated time: Asychronous cells
|
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 |
7018-1-2.withdup.j.r.Eblacklist.q0.05.narrowPeak 7018-MB-2
|
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 |
SAMN32103919 |
SRA |
SRX18534299 |