|
| Status |
Public on Feb 10, 2023 |
| Title |
DAXX_ChIP_CTRL_B_lymphocytes_IgGCTRL |
| Sample type |
SRA |
| |
|
| Source name |
Human B lymphocytes
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Human B lymphocytes
disease state: healthy control
chip antibody: anti-IgG
|
| Growth protocol |
human B lymphocytes were cultured in RPMI 1640 medium containing 15% FBS. Medium was exchanged every other day.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin immunoprecipitation (ChIP) was performed by using a CHIP assay kit (Millipore Sigma, 17-295).
The ChIP-seq libraries were prepared using an NEBNext Ultra II FS DNA Library Prep kit (NEB, E6177S).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Raw reads were processed with TrimGalore v0.6.7 and controlled for quality with FastQC v.0.11.9.
The trimmed reads were aligned to the human genome (hg19) using Bowtie2 v2.3.5.1.Uniquely mapped reads were retained to identify DAXX-associated peaks using MACS2 v2.2.6 with standard parameters (q-value cutoff 0.05).
Assembly: hg19
Supplementary files format and content: Peaks were annotated and visualized with an R package, ChIPseeker
|
| |
|
| Submission date |
Jan 20, 2023 |
| Last update date |
Feb 10, 2023 |
| Contact name |
Yang Liu |
| E-mail(s) |
liuyang19870210@outlook.com
|
| Organization name |
Johns Hopkins University
|
| Department |
Biochemistry and Molecular Biology
|
| Lab |
Wang Lab
|
| Street address |
615 N. Wolfe Street
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21211 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE223259 |
Chromatin accessibilities in C9HRE ALS/FTD patient cells |
| GSE223401 |
Profiling the genomic binding of DAXX in C9HRE ALS/FTD patient cells |
|
| Relations |
| BioSample |
SAMN32818719 |
| SRA |
SRX19123218 |
