|
| Status |
Public on Jun 17, 2020 |
| Title |
WT H3Ac_ChIPSeq Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
S. aureus infected orthopedic implant-associated tissue
|
| Organism |
Mus musculus |
| Characteristics |
cell type: MDSCs
strain: C57BL/6
age: 10-12 weeks
infected with: WT S. aureus
chip antibody: Histone H3ac (pan-acetyl, pAb) antibody (Active motif Cat no. 61537)
s. aureus background strain and genotype: USA300 LAC13c
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Soft tissues surrounding S. aureus-infected implants were removed, homogenized and stained for FACS. Live MDSCs from WT and triple mutant-infected animals were sorted and chromatin isolated from each sample.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Adaptor sequences and low quality (Phred score < 20) ends were trimmed from sequences using Trim Galore software package (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Resulting fastq files were aligned to the human genome (GRCm38/mm10) using the sequence aligner Bowtie2 (version 2.2.3).
Picard routine MarkDuplicates (http://broadinstitute.github.io/picard/) was used to remove sequence duplications.
Peak calling, of ChIP enriched regions the THOR peak caller software of each ChIP to corresponding input DNA sample was used to determine binding regions based on a FDR adjusted p-value (q-value) <0.05.
BigWig files were generated using the deeptools bamCoverage routine (https://deeptools.readthedocs.io/en/develop/).
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files were generated using the resulting bam files and deeptools bamCoverage routine (https://deeptools.readthedocs.io/en/develop/).
|
| |
|
| Submission date |
Aug 07, 2019 |
| Last update date |
Jun 17, 2020 |
| Contact name |
Adam R. Karpf |
| E-mail(s) |
adam.karpf@unmc.edu
|
| Phone |
402-559-6115
|
| Organization name |
University of Nebraska Medical Center
|
| Department |
Eppley Institute for Research in Cancer
|
| Street address |
985950 Nebraska Medical Center
|
| City |
Omaha |
| State/province |
Nebraska |
| ZIP/Postal code |
68198-5950 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE135494 |
Lactate production by Staphylococcus aureus biofilm inhibits HDAC11 to reprogramme the host immune response during persistent infection [ChIP-seq] |
| GSE135496 |
Lactate production by Staphylococcus aureus biofilm inhibits HDAC11 to reprogramme the host immune response during persistent infection |
|
| Relations |
| BioSample |
SAMN12518061 |
| SRA |
SRX6665829 |
