|
| Status |
Public on Jul 03, 2024 |
| Title |
H3K4Me2_CD56Br_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
peripheral blood
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: FACS-purified lymphocytes
antibody: anti-H3K4Me2, Abcam ab32356
|
| Treatment protocol |
NA
|
| Growth protocol |
NA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Human peripheral blood mononuclear cells (PBMC) from peripheral blood were isolated by Ficoll-Paque density gradient centrifugation. Cells were isolated by FACS (viable CD45+ Lin- (CD3- CD4- CD5- TCRαβ- TCRγδ- CD14- CD19-) CD7+ CD56-high CD16- or CD56-dim CD16+ cells)
Nextera DNA library construction (as described in Schmidl et al. Nature Methods 2015).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were aligned using bowtie 2 using default parameters.
Sorted and indexed bam files were parsed to HOMER to creat tag directories without duplicates and bedgraphs for browser visualization.
HOMER was used to identify enriched regions ('peak calling') using findPeaks with -region -size 1000 -minDist 2500 options
Genome_build: hg19
Supplementary_files_format_and_content: HOMER peak calling files
|
| |
|
| Submission date |
Mar 01, 2019 |
| Last update date |
Jul 03, 2024 |
| Contact name |
Ralph Stadhouders |
| E-mail(s) |
stadhoudersralph@gmail.com
|
| Organization name |
Erasmus Medical Center
|
| Department |
Pulmonary Medicine
|
| Street address |
Dr. Molewaterplein 50
|
| City |
Rotterdam |
| ZIP/Postal code |
3015 GE |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE127721 |
Epigenetic profiling of primary human peripheral blood NK cell populations |
|
| Relations |
| BioSample |
SAMN11041866 |
| SRA |
SRX5447845 |
