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Sample GSM3719107 Query DataSets for GSM3719107
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

Supplementary file Size Download File type/resource
GSM3719107_H3K36me3_jmjd1c_del2.mm10.norm-RPM.bigwig 257.5 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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