|
| Status |
Public on Nov 17, 2019 |
| Title |
MAC7d_Input-ChIP_donorP |
| Sample type |
SRA |
| |
|
| Source name |
MAC7d_Input-ChIP
|
| Organism |
Homo sapiens |
| Characteristics |
donr id: donorP
tissue/cell type: MO-derived
cell subtype: primary monocyte-derived macrophages
chip antibody: none
|
| Growth protocol |
Peripheral blood monocytes were separated by leukapheresis of healthy donors, followed by density gradient centrifugation over Ficoll/Hypaque and subsequent counter current centrifugal elutriation in a J6M-E centrifuge. Monocytes were > 85% pure as determined by morphology and expression of CD14 antigen. To generate macrophages, isolated monocytes were cultured in endotoxin-free RPMI 1640 medium supplemented with vitamins, antibiotics, pyruvate, nonessential amino acids, 5 x 10-8 M beta-mercaptoethanol, 2% human pooled AB-group serum on teflon foils for 7 days.
Collection of blood cells from healthy donors was performed in compliance with the Helsinki Declaration. All donors signed an informed consent. The leukapheresis procedure and subsequent purification of hematopoietic cell types were approved by the local ethical committee (reference number 12-101-0260). Human mast cell were purified from skin that was obtained from cosmetic breast-reduction surgeries (Motakis et al., 2014) with informed consent of the patients. Mast cell preparations were performed in compliance with the Helsinki Declaration, and approved by the ethics committee of the Charité Universitätsmedizin Berlin (reference number EA1/204/10).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIPseq was essentially done as described (Pham et al. 2012).
Libraries were generated as described (Pham et al. 2012)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
Chromatin input (control)
|
| Data processing |
Raw data were aligned to the human genome (GRCh37/hg19) using bowtie2 (Langmead and Salzberg, 2012) in very sensitive mode, keeping only reads that map to a single unique genomic location for further analysis (MAPQ > 10).
Bigwigs of ChIPseq data sets were generated using HOMER v4.9 (Heinz et al, 2010) and standard settings. For cancer cell lines, we used the Control-FREEC v11.0 program to determine allelic imbalances from low-depth whole genome sequencing data and corrected ChIP-seq read counts accordingly to generate CNV-corrected bigWigs.
ChIP-seq peaks were called using HOMER?s findPeaks program in ??factor?? mode using default parameters (standard) or with -fdr 0.00001 (stringent) to identify focal peaks. Stringent peaks were further filtered for a minimal normalized tag count of 15 tags per peak. All peak sets were filtered by subtracting blacklisted genomic regions 49, and by filtering out regions with a mappability <0.8. The latter was annotated to peak regions from mappability tracks generated with the GEM package using HOMER?s annotatePeaks.pl.
Genome_build: hg19
Supplementary_files_format_and_content: ChIPseq tracks in bigWig format (before and after CNV normalization
Supplementary_files_format_and_content: ChIPseq peaks (called using standard or stringent parameters)
|
| |
|
| Submission date |
Mar 25, 2019 |
| Last update date |
Nov 19, 2019 |
| Contact name |
Michael Rehli |
| E-mail(s) |
michael.rehli@klinik.uni-r.de
|
| Organization name |
University Hospital Regensburg
|
| Department |
Internal Med III
|
| Street address |
F.-J.-Strauss-Allee 11
|
| City |
Regensburg |
| ZIP/Postal code |
93042 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21290 |
| Series (2) |
| GSE128834 |
The hematopoietic master transcription factor PU.1 requires its interaction with the SWI/SNF remodeler to access chromatin de novo [ChIP-seq] |
| GSE128837 |
The hematopoietic master transcription factor PU.1 requires its interaction with the SWI/SNF remodeler to access chromatin de novo |
|
| Relations |
| BioSample |
SAMN11252786 |
| SRA |
SRX5574378 |
