|
| Status |
Public on Apr 02, 2019 |
| Title |
H3K9me3 knockout LSK cells |
| Sample type |
SRA |
| |
|
| Source name |
Haematopoietic stem cell
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL6
genotype: Kdm4a, b c triple knockout
cell type: LSK cell
chip antibody: anti_H3K9me3 (Abcam: ab9898)
|
| Treatment protocol |
Conditional knockout mice and control mice were injected with tamoxifen. After two weeks LSK cells were FACS sorted from the bone marrow
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Extraction protocol: Immunoprecipitation of formaldehyde cross-linked and sonicated cell lysate
Library construction protocol: NEBNext Ultra II protocol (NEB, E7645S)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Trimmed with Trimmomatic: IlluminaClip; Crop to 73; SLIDINGWINDOW across 4 bases, average quality required 20
Mapped with Bowtie2 against mm10 using using (--sensitive) preset settings. Duplicates removed with rmdup.
H3K4me3 data was taken from GSE55850 (i.e., third-party reanalysis of Samples GSM1347235 GSM1347236).
H3K9me3 reads were quantified +/- 500bp from H3K4me3 positive TSSs using EaSeq software (http://easeq.net). Reads from WT and knockout were divided to get the fold change in H3K9me3 levels after induction of knockout.
Genome_build: mm10
Supplementary_files_format_and_content: An excel file containing the positions of the H3K4me3 peaks and quantified H3K9me3 levels at H3K4me3 positive TSSs.
|
| |
|
| Submission date |
Apr 01, 2019 |
| Last update date |
Apr 02, 2019 |
| Contact name |
Karl Agger |
| E-mail(s) |
karl.agger@bric.ku.dk
|
| Phone |
+4522832639
|
| Organization name |
University of Copenhagen
|
| Department |
BRIC
|
| Street address |
Ole Maaloes Vej 5
|
| City |
Copenhagen |
| ZIP/Postal code |
2200 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE129156 |
Genome-wide maps of H3K9me3 in hematopoietic stem cells from Kdm4a, b, c triple knockout mice |
| GSE129157 |
The KDM4/JMJD2 histone demethylases are required for hematopoietic stem cell maintenance |
|
| Relations |
| BioSample |
SAMN11309525 |
| SRA |
SRX5620961 |
