|
| Status |
Public on Jun 17, 2024 |
| Title |
SON_Control |
| Sample type |
SRA |
| |
|
| Source name |
Lung Tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Lung Tissue
cell line: IMR90
cell type: Human Embryonic Fibroblast
treatment: untreated (control)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For SON ChIPmentation, cells were extracted and fixed at room temperature with 1% formaldehyde for 10 minutes. For HMGB2 ChIPmentation, cells were initially fixed with 1.5 mM EGS at room temperature for 20 minutes 1% formaldehyde for 10 minutes followed by incubation with
Antibody incubation, washes, Tagmentation and DNA extraction were performed as described in the methods section
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Basecalls were performed using bcl2fastq v2.17 for NextSeq550 output.
Paired-end reads were processed for adapter removal and mapped to the hg38 reference genome using Bowtie2.
RPKM normalized bigwigs were generated using deeptools.
Peaks were called using macs2. For HMGB2 the significant cut-off was q-value 0.03. For the SON default parameters were applied
Peak consistency between replicates was evaluated using IDR and p-value ranking
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak
|
| |
|
| Submission date |
Jun 14, 2024 |
| Last update date |
Jun 17, 2024 |
| Contact name |
Argyris Papantonis |
| E-mail(s) |
argyris.papantonis@med.uni-goettingen.de
|
| Organization name |
University Medical Center Göttingen
|
| Department |
Institute of Pathology
|
| Street address |
Robert-Koch-Str. 40
|
| City |
Göttingen |
| ZIP/Postal code |
37075 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE269858 |
Repurposed nuclear speckle and mitosis components induce CTCF clustering to sustain the senescence splicing program [ChIPmentation] |
|
| Relations |
| BioSample |
SAMN41834479 |
| SRA |
SRX24925855 |
