|
Status |
Public on Jan 16, 2024 |
Title |
H2BK120ac Cut&Run shCtrl_Eto |
Sample type |
SRA |
|
|
Source name |
Bone Marrow
|
Organism |
Homo sapiens |
Characteristics |
tissue: Bone Marrow cell line: U2OS cell type: osteosarcoma cell line genotype: Dox inducible shCtrl treatment: Dox, 1µg/ml, 24 h; 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
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|
|
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
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|
|
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 |
SAMN36379358 |
SRA |
SRX20959151 |