2025-04-21
ENA first public
ERC000011
ENA-CHECKLIST
Institut für Virologie TUM School of Medicine and Health Technische Universität München
INSDC center name
public
INSDC status
ERS23956202
SRA accession
E-MTAB-14995:wap_chip_r2
Submitter Id
ArrayExpress
broker name
macrophage dendritic cell progenitor
cell type
not collected
collection date
human
common name
Protocols: Macrophages (3–10 x 10⁶ cells per condition, 2–3 biological replicates/macrophage donors per condition) were washed once with warm PBS and incubated for 30 min at 37°C with accutase (eBioscience) to detach the cells. For ChIP, BSA-blocked ChIP grade protein A/G magnetic beads (Thermo Fisher Scientific) were added to the chromatin and antibody mixture and incubated for 2 h at 4°C rotating to bind chromatin-antibody complexes. Samples were incubated for ~3 min with a magnetic stand to ensure attachment of beads to the magnet and mixed by pipetting during the wash steps. Eluted DNA was subjected to ChIP-seq library preparation. Input chromatin DNA was prepared from 1/4 of the chromatin amount used for ChIP. Antibodies used for ChIP were anti-H3S10ph (Invitrogen, 9H12L10, 6 μl (3 μg) per ChIP) and anti-H3K9me3S10ph (Abcam, ab5819, 2 μg per ChIP). ChIP-seq libraries were constructed with 1–10 ng of ChIP DNA or input control as starting material. Libraries were generated using the NEXTflex ChIP-Seq Kit (Bioo Scientific) following the manufacturer’s recommendations. Concentrations of all samples were measured with a Qubit Fluorometer (Thermo Fisher Scientific), and fragment length distribution of the final libraries was analyzed with the DNA High Sensitivity Chip on an Agilent 2100 Bioanalyzer (Agilent Technologies). All samples were normalized to 2 nM and pooled equimolar.
description
not collected
geographic location (country and/or sea)
Yersinia enterocolitica WAP
infect
not applicable
isolate
Homo sapiens
organism
Homo sapiens
organism
Homo sapiens
scientific_name
wap_chip_r2
title