|
| Status |
Public on Aug 20, 2020 |
| Title |
JM105: Adult HSC H3K4me1-2 ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
Hematopoietic Stem Cell
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Hematopoietic Stem Cell
histone_mark: H3K4me1
age: 8 week old
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
HSCs and HPCs were soted and then fixed for chromatin isolation per Schmidl et l., Nature Methods 10:963.
Chipmentation - Chromatin isolation with the indicated antibody followed by tagmentation with Tn5 as per Schmidl et l., Nature Methods 10:963.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Adult_HSC_H3K4me1
processed data in series file Adult_HSC_H3K4me1.pooled.fc.signal.bigwig
processed data in series file Adult_HSC_H3K4me1.filt.narrowPeak.gz
|
| Data processing |
Sequencing reads were demultiplexed and aligned to mouse genome (mm10) by novoalign (versoin 3.04.06)
Signal strength relative to the control samples were generated using MACS2.
Optimal set of peaks were generated using the Kundaje lab AQUAS TF and histone ChIP-seq pipeline (https://github.com/kundajelab/chipseq_pipeline version 0.33)
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: bigwig, narrowPeak
|
| |
|
| Submission date |
Mar 24, 2019 |
| Last update date |
Aug 20, 2020 |
| Contact name |
Jeffery Magee |
| E-mail(s) |
magee_j@kids.wustl.edu
|
| Organization name |
Washington University School of Medicine
|
| Department |
Internal Medicine - Cardiovascular Division
|
| Street address |
660 S Euclid Ave.
|
| City |
St Louis |
| State/province |
Missouri |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE128760 |
Neonatal hematopoietic stem and progenitor cell ontogeny at single cell resolution (ChIP-seq) |
| GSE128762 |
Neonatal hematopoietic stem and progenitor cell ontogeny at single cell resolution |
|
| Relations |
| BioSample |
SAMN11245175 |
| SRA |
SRX5565534 |
