|
| Status |
Public on Apr 12, 2019 |
| Title |
H3K9me3_3511_CRE_ChIP |
| Sample type |
SRA |
| |
|
| Source name |
Mouse primary leukemia
|
| Organism |
Mus musculus |
| Characteristics |
cell type: MLL-AF9 leukemia cells
chip antibody: H3K9me3(ab8898)
|
| Growth protocol |
MLL-AF9 leukemia cells were cultured in RPMI media supplemented with 10% FBS 1% P/S and 10ng/ml mIL3.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K36Me3, H3K27Me3, H3K9me3, or H3K9me1 antibody.
Libraries were prepared using standard NEBNext Ultra I/II DNA Library Prep Kit for Illumina (#E7370S) (#E7645S)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Samples were demultiplexed and FastQ files were generated using Illumina BaseSpace
The BasePairTech.com ChIP-seq pipeline was used for analysis
Reads were trimmed using trim galore to remove adapters and read ends with phred quality scores < 15
Reads were aligned to the mm10 genome using bowtie2
Duplicate reads were removed using Picard tools and bigwig files were created representing coverage per million reads mapped
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files represent ChIP-seq coverage across the genome per one million reads mapped
|
| |
|
| Submission date |
Apr 11, 2019 |
| Last update date |
Mar 08, 2022 |
| Contact name |
Nan Zhu |
| E-mail(s) |
nan.zhu@versiti.org
|
| Organization name |
Versiti Blood Research Institute Milwaukee
|
| Street address |
8733 W Watertown Plank Rd
|
| City |
Milwaukee |
| State/province |
WI |
| ZIP/Postal code |
53226 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE129661 |
ChIP-seq of histone marks H3K36, H3K27, and H3K9 in JMJD1C knockout or mutated MLL-AF9 leukemia cells |
| GSE129675 |
Critical Role of Jumonji Domain of JMJD1C in MLL-rearranged leukemia |
|
| Relations |
| BioSample |
SAMN11398975 |
| SRA |
SRX5669833 |
