|
| Status |
Public on Jan 16, 2024 |
| Title |
H2BK120ac Cut&Run shNONO_Eto with mCherryNONO rescue |
| Sample type |
SRA |
| |
|
| Source name |
Bone Marrow
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Bone Marrow
cell line: U2OS
cell type: osteosarcoma cell line
genotype: siNONO transfection, 24h ; mCherry NONO transfection, 24h
treatment: Eto, 20µM, 2h
antibody: H2BK120ac
|
| Treatment protocol |
Treatment as indicated
|
| Growth protocol |
Cells were grown in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cut&Run DNA
Cut&Run DNA was used for library preparation with NEBNext Ultra II Directional DNA Library Prep kit. The libraries were amplified with 12-16 PCR cycles depending on the input DNA. The concentration and size distribution of the libraries were determined on a Fragment Analyzer using the NGS Fragment High Sensitivity Analysis Kit (1-6,000 bp; Agilent Technologies). The libraries were sequenced on the NextSeq2000 Illumina platform for 75 cycles. Base calling was performed using Illumina’s BaseSpace platform
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
Fastq files were generated Illumina’s BaseSpace platform and overall sequencing quality was analyzed with the FastQC script.
For Cut&Run-seq, reads were mapped to hg19 and E.coli withBowtie2, and then normalized based on E.coli reads or on read depth.
Assembly: hg19
Supplementary files format and content: bedgraph
Library strategy: Cut&Run
|
| |
|
| Submission date |
Jul 10, 2023 |
| Last update date |
Jan 16, 2024 |
| Contact name |
Martin Eilers |
| Organization name |
University of Wuerzburg
|
| Department |
Chair for Biochemistry and Molecular Biology
|
| Lab |
Martin Eilers
|
| Street address |
Am Hubland
|
| City |
Wuerzburg |
| ZIP/Postal code |
97074 |
| Country |
Germany |
| |
|
| Platform ID |
GPL30173 |
| Series (2) |
| GSE236899 |
Nucleolar detention of NONO shields DNA double-strand breaks from aberrant transcripts [CUT&RUN] |
| GSE236900 |
Nucleolar detention of NONO shields DNA double-strand breaks from aberrant transcripts |
|
| Relations |
| BioSample |
SAMN36379361 |
| SRA |
SRX20959148 |
