|
| Status |
Public on May 02, 2012 |
| Title |
MAC H2AZ |
| Sample type |
SRA |
| |
|
| Source name |
Monocyte-derived macrophage
|
| Organism |
Homo sapiens |
| Characteristics |
chip antibody: H2AZ
cell type: Monocyte-derived macrophage
|
| 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 up to 7 days.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA from chromatin immunoprecipitation (10-50ng) was adapter-ligated and PCR amplified using Illumina kit Preparing samples for ChIP sequencing of DNA (IP-102-1001) following the manufacturerâs protocol. ChIP fragments were sequenced for 36 cycles on Illumina Genome Analyzers I or II according to the manufacturerâs instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
Chromatin IP against H2AZ
|
| Data processing |
Sequence tags were mapped to the current human reference sequence (GRCh27/hg19) using Bowtie and only uniquely mapped tags were used for downstream analyses. Except for EGR2 where only one donor was used (sample 12) all other samples represent combined data from 2-3 donors. Tag counts were normalized to 1e7 specifically mapped tags. Local tag counts were GC-normalized to match the corresponding monocyte data sets using HOMER.
|
| |
|
| Submission date |
Aug 23, 2011 |
| Last update date |
May 15, 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 |
GPL9052 |
| Series (1) |
| GSE31621 |
Dynamic epigenetic enhancer signatures are predictive for key transcriptional regulators associated with cellular differentiation states |
|
| Relations |
| SRA |
SRX093187 |
| BioSample |
SAMN00714115 |
