|
| Status |
Public on Jul 21, 2023 |
| Title |
Kacme_293T_2 |
| Sample type |
SRA |
| |
|
| Source name |
Human embryonic kidney derived cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293T cells
antibody: In house Kacme
treatment: None
experiment: ChIP-seq
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
20-30 million cells per IP were crosslinked with formaldehyde for 10 minutes. Nuclei were sonicated, lysates were clarified, and histone-DNA complexes were isolated with antibody.
Libraries were prepared using standard Illumina protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Kacme_293T_2
|
| Data processing |
Reads were trimmed of adaptor sequences using Cutadapt.
Reads were aligned to dm6 or hg38 genome using Bowtie2 v2.2.9.
Peaks were called using MACS2 with default parameters.
Fold enrichment bigwig tracks were created using MACS2 bdgcamp compared to input control.
Assembly: dm6, hg38
Supplementary files format and content: bigwig files of fold enrichment tracks over input control
Supplementary files format and content: narrowPeak peak files from MACS2
|
| |
|
| Submission date |
Sep 14, 2022 |
| Last update date |
Jul 21, 2023 |
| Contact name |
Matthew Simon |
| E-mail(s) |
matthew.simon@yale.edu
|
| Organization name |
Yale University
|
| Department |
Molecular Biophysics and Biochemistry
|
| Street address |
100 West Campus Drive, Ste MIC 231
|
| City |
Orange |
| State/province |
CT |
| ZIP/Postal code |
06477 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE182204 |
Acetyl-methyllysine marks chromatin at active transcription start sites |
|
| Relations |
| BioSample |
SAMN30844525 |
| SRA |
SRX17564626 |
