|
| Status |
Public on Aug 04, 2022 |
| Title |
H3K27ac_Panob_2 |
| Sample type |
SRA |
| |
|
| Source name |
Neuroblastoma cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Neuroblastoma cells
treatment: Panobinostat
chip antibody: H3K27ac (Abcam ab4729)
cell line: GI-ME-N
|
| Treatment protocol |
24h after seeding, adherent cells were treated with solvent (DMSO) or 30 nM panobinostat for 18 h.
|
| Growth protocol |
Cells were grown under standard conditions in a humidified atmosphere at 37°C and 5% CO2
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated samples and histone-DNA complexes were isolated with antibody. Genomic DNA was extracted and purified using Qiagen PCR Purification Kit according to standard instructions
Libraries were prepared with the NEBNext® ChIP-Seq Library Prep Reagent Set for Illumina (10 ng input) following the manufacturers’ instructions. A size selection step for fragments of 300 bp length was performed after library preparation. Pools of six to seven libraries were sequenced on one lane HiSeq 4000 in 50 single read mode.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Neuroblastoma cells, treated with Panobinostat, antibody H3K27ac (Abcam ab4729)
|
| Data processing |
Reads were aligned to the human genome version GRCh38 using the program subread v. 1.6.4
Peaks were called using the program MACS2 v. 2.26 using the input samples as controls
Differential peak binding was determined separately for each probe with R package DiffBind v. 2.10.0 with the following settings: minOverlap=3, summits=50, filterFun=max (and otherwise default options)
For peak annotation, R packages ChIPSeeker v. 1.18.0 and TxDb.Hsapiens.UCSC.hg38.knownGene v. 3.4.0 were used
Genome_build: GRCh38
Supplementary_files_format_and_content: BED files: position of peaks identified with MACS2
|
| |
|
| Submission date |
Aug 04, 2020 |
| Last update date |
Jan 06, 2023 |
| Contact name |
January 3rd Weiner |
| E-mail(s) |
january.weiner@gmail.com
|
| Phone |
030450543049
|
| Organization name |
Berlin Institute of Health, Charité Medical University of Berlin
|
| Department |
CUBI
|
| Street address |
Charitéplatz 1
|
| City |
Berlin |
| ZIP/Postal code |
10117 |
| Country |
Germany |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE155705 |
HDAC inhibition suppresses telomerase activity in neuroblastoma cells harboring TERT rearrangements [ChIP-Seq] |
| GSE155707 |
HDAC inhibition suppresses telomerase activity in neuroblastoma cells harboring TERT rearrangements |
|
| Relations |
| BioSample |
SAMN15731380 |
| SRA |
SRX8887748 |
