|
| Status |
Public on Jan 08, 2025 |
| Title |
Input_RBPJ_KO_42_HaloRBPJ_K195E |
| Sample type |
SRA |
| |
|
| Source name |
HeLa
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
genotype: RBPJ_KO_42_HaloRBPJ_K195E
|
| Growth protocol |
Human HeLa cells were grown at 37°C with 5% CO2 in DMEM medium supplemented with 2% FCS and penicillin/streptomycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was done essentially as previously described (Giaimo et al. Jove 2017, doi: 10.3791/55907).
Lybrary-prep kit for ChIP-Seq: Diagenode MicropPlex Library Preparation kit v3.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The fastq files were quality and adapter trimmed using TrimGalore.
The fastq files were aligned using Hisat2.
Duplicated reads were removed using Picard tools.
bigWig files were generated using bamCoverage.
Peak calling was done using Peakranger v.1.18 with a q-value cutoff < 0.0001. Peaks had be conserved in both replicates.
Assembly: hg19
Supplementary files format and content: Peaks as .bed files (generated from both replicates, and linked to the corresponding *_1 sample records)
Supplementary files format and content: Normalized coverage tracks as .bigwig files
|
| |
|
| Submission date |
Dec 12, 2023 |
| Last update date |
Jan 08, 2025 |
| Contact name |
Tobias Friedrich |
| E-mail(s) |
tobias.friedrich@pennmedicine.upenn.edu
|
| Organization name |
University of Pennsylvania
|
| Street address |
421 Curie Boulevard
|
| City |
Philadelphia |
| State/province |
Pennsylvania |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE249973 |
Dependence of RBPJ genomic binding on the formation of macromolecular complexes |
|
| Relations |
| BioSample |
SAMN38779927 |
| SRA |
SRX22865515 |
