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| Status |
Public on Apr 24, 2023 |
| Title |
U2OS33_T2h_H3K27ac_Rep3 |
| Sample type |
SRA |
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| Source name |
U2OS
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| Organism |
Homo sapiens |
| Characteristics |
cell line: U2OS
integrated construct: H3.3 FLAG
hours post_infection: T2h
chip antibody: H3K27ac
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were crosslinked with 1% formaldehyde for 10 min at room temperature and the reaction was quenched with glycine at a final concentration of 0.125 M. Chromatin was sheared using ultrasonication (Covaris S2). A total of 2.5 µg of antibody against H3K27ac (Abcam, ab4729), or FLAG (M2, Sigma Aldrich, F3165), was bound to 20 µl pre-washed Dynabeads Protein A (Thermo Fisher Scientific) in a total volume of 200 µl PBS containing 0.02% Tween-20 for 1h at room temperature rotating at 6 rpm. The buffer was removed on a magnet and antibody-coupled beads were resuspended in 120µl dilution buffer (20mM Tris pH7.4, 2mM EDTA, 100mM NaCl, 0.5% Triton x-100) containing proteinase inhibitors (cOmplete™, EDTA-free Protease Inhibitor Cocktail, 50x, Sigma). 80µl sonicated chromatin was added to the antibody-coupled Dynabeads (sonicated chromatin of approx. 1.7x106 cells) and incubated for 3h at room temperature rotating at 6 rpm. Beads were washed on a magnet and chromatin was eluted. After crosslink reversal, RNase A and proteinase K treatment, DNA was extracted with the Monarch PCR & DNA Cleanup kit (NEB).
Sequencing libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) according to manufacturer’s instructions
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 550 |
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| Data processing |
Paired-end reads were mapped to the reference using bowtie2-aligner with following paramters: --very-sensitive-local, --no-discordant
Reads were filtered to mapping quality > 30 and only reads mapped in proper pair were kept using samtools.
CPM-normalized coverage tracks were generated using the bamCoverage script of the deepTools package
Assembly: hg19 and AY339865.1 (adapted)
Supplementary files format and content: bigwig files showing CPM normalized coverage
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| Submission date |
Nov 22, 2022 |
| Last update date |
Apr 24, 2023 |
| Contact name |
Uwe Schwartz |
| E-mail(s) |
uwe.schwartz@ur.de
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| Organization name |
University of Regensburg
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| Department |
NGS Analysis Center
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| Street address |
Universitätstraße 32
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| City |
Regensburg |
| ZIP/Postal code |
93053 |
| Country |
Germany |
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| Platform ID |
GPL21697 |
| Series (2) |
| GSE136550 |
Changes in adenoviral chromatin organization precede early gene activation |
| GSE218541 |
Changes in adenoviral chromatin organization precede early gene activation [ChIP-Seq] |
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| Relations |
| BioSample |
SAMN31836763 |
| SRA |
SRX18348481 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6751583_Rep3_U2OS33_T2h_H3K27ac.bw |
64.9 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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