|
Status |
Public on Apr 12, 2019 |
Title |
H3K36me3_3511_CRE_ChIP |
Sample type |
SRA |
|
|
Source name |
Mouse primary leukemia
|
Organism |
Mus musculus |
Characteristics |
cell type: MLL-AF9 leukemia cells chip antibody: H3K36me3 (abcam9050)
|
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 |
SAMN11398988 |
SRA |
SRX5669821 |