|
| Status |
Public on Mar 19, 2017 |
| Title |
H3K4Me2_ILCP_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
peripheral blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: peripheral blood
cell type: Innate lymphoid cell precursors (ILCPs)
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 (ILCP: viable CD45+ Lin- (CD3- CD4- CD5- TCRαβ- TCRγδ- CD14- CD19-) CD7+ CD127+ CRTh2- CD117+ cells, HSC: CD45+ CD34+)
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 |
Nov 29, 2016 |
| Last update date |
May 15, 2019 |
| 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) |
| GSE90640 |
Systemic human ILC precursors provide a substrate for tissue ILC differentiation |
|
| Relations |
| BioSample |
SAMN06067811 |
| SRA |
SRX2380901 |
