|
| Status |
Public on May 27, 2024 |
| Title |
HEK293 cells, Flag-ENL-WT, DMSO, ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
HEK293
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293
treatment: DMSO
|
| Treatment protocol |
Cells were treated with DMSO or TDI-11055 (10 μM) for 24 hrs
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq sample libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit (NEB, #E7645L) following the manufacturer's instructions. After adapter ligation, DNA was PCR amplified with Illumina primers for indicated cycles and the DNA size distribution was quantified on an Agilent Bioanalyzer DNA chip ( Agilent, #5067-1504).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
ChIP-seq and CUT&Tag samples were sequenced using Illumina NextSeq 550.
Raw reads were mapped to the mouse reference genome (hg19) and transcriptome using Bowtie2 v 2.2.5 with default parameters.
Aligned BAM files were sorted using function samtools v 1.6. Secondary alignments, unmapped reads, and duplicate reads in the sorted bam files were filtered out using samtools v 1.6. The filtered and sorted bam files were then indexed using function indexBam from samtools v 1.6.
Peaks were called using MACS v 2.2.8, peaks were called at q ≤ 1E−10.
Filtered, sorted, indexed BAM files were converted to bigwig files using bamCoverage from deeptools v 3.5.2
Assembly: hg19
Supplementary files format and content: bigWig files are in an indexed binary format
|
| |
|
| Submission date |
Sep 22, 2023 |
| Last update date |
May 27, 2024 |
| Contact name |
Liling Wan |
| E-mail(s) |
wanlabepigenetics@gmail.com
|
| Organization name |
University of Pennsylvania
|
| Department |
Cancer Biology
|
| Lab |
Wanlab
|
| Street address |
421 Curie Blvd
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL21697 |
| Series (2) |
| GSE243866 |
Single-Cell multi-omics reveals disrupted gene regulatory landscape and cell differentiation by Wilms tumor-associated ENL mutation in the developing kidney (ChIP-Seq) |
| GSE243871 |
Single-Cell multi-omics reveals disrupted gene regulatory landscape and cell differentiation by Wilms tumor-associated ENL mutation in the developing kidney |
|
| Relations |
| BioSample |
SAMN37519099 |
| SRA |
SRX21864882 |
