|
| Status |
Public on Jun 20, 2024 |
| Title |
HDGF ChIP, ctrl depletion, HEK293T, Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
HEK293T
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293T
cell type: Human embryonic kidney
genotype: Wild type
chip antibody: HDGF (Proteintech, #11344-1-AP)
|
| Growth protocol |
HEK293T cells were maintained in DMEM supplemented with 10% fetal calf serum (FCS) and antibiotics in a humidified atmosphere with 5% CO2 at 37C. For starvation conditions, cells were grown in glucose-free medium for 24 hours before harvesting. For HDGF depletion, HDGF was depleted using HDGF-specific siPOOLs for 72 hours before harvesting.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed using 1% formaldehyde for 5 min. The crosslinking reaction was quenched with 125mM glycine. Cells were lysed in swelling buffer 5mM PIPES pH8; 85mM KCL; 0,5% IGEPAL + protease inhibitors). Chromatin was sonicated on a Diagenode Bioruptor300 for 30 min (30s ON/ 30s OFF) on the high setting.
At least 20 mg of DNA were used for library preparation using the NEBNext Ultra DNA library prep kit.
ChIPseq, 150 bp paired-end reads
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq X Plus |
| |
|
| Data processing |
FastQC quality control, Trimmomatic adapter trimming (parameters: ILLUMINACLIP:NexteraPE-PE.fa:1:30:4:1:true TRAILING:3 MINLEN:20)
Bowtie alignment (parameters: -X2000 (maximal fragment length) and -very-sensitive)
Removal of duplicate reads and reads with map quality score <10 with Picard tools
MACS2 peak calling with q-value<0.05
Assembly: hg38
Supplementary files format and content: bigwig files contain reads normalized by total library size (RPKM)
Supplementary files format and content: narrow.peak files contain MACS2 called peaks based on two replicates, using the respective input sample as a control
|
| |
|
| Submission date |
Feb 28, 2024 |
| Last update date |
Jun 20, 2024 |
| Contact name |
Stefanie Jonas |
| E-mail(s) |
stefanie.jonas@mol.biol.ethz.ch
|
| Organization name |
ETH Zurich
|
| Department |
Biology
|
| Street address |
Otto-Stern-Weg 5
|
| City |
Zürich |
| State/province |
Zürich |
| ZIP/Postal code |
8093 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL34284 |
| Series (2) |
| GSE233958 |
Basis of gene-specific transcription regulation by the Inegrator Complex |
| GSE260520 |
Basis of gene-specific transcription regulation by the Inegrator Complex (ChIP-Seq II) |
|
| Relations |
| BioSample |
SAMN40194889 |
| SRA |
SRX23787630 |
