NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1569546 Query DataSets for GSM1569546
Status Public on Apr 30, 2015
Title D544R_H3K79me3
Sample type SRA
 
Source name Hematopoietic progenitor cells
Organism Mus musculus
Characteristics cell-type: Primary Hematopoietic progenitor cells
genotype/variation: MLL-AF9 (D544R)
chip antibody: H3K79me3, Diagenode cat#pAb-068-050
Extracted molecule genomic DNA
Extraction protocol Cross-linked cells were sonicated go get 300bp average fragments and incubated with either H3K79me2 or H3K79me3 antibodies.
For DNA sequencing, approximately 0.5-3 ng ChIP-DNA was processed for whole genome library preparation using Illumina TruSeq Chip Library Kit according to the manufacturer’s protocol.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina MiSeq
 
Description BAM files were final files used for analyses and include reads from multiple runs that were merged
Data processing The sequencing reads from Illumina MiSeq were aligned to mouse mm9 genome using the BOWTIE alignment tool. These aligned reads were then processed and converted into BigWig format, which were loaded in the UCSC Genome browser for visualization. Reads from multiple runs were merged. BEDTOOLS suite commands were used for format conversions and the reads were converted to BED format. To identify genes enriched for H3K79me2 and H3K79me3, we calculated the total number of reads in the gene body regions for each gene. To calculate the enrichments, Transcription Start Site (TSS) and Transcription End Site (TES) coordinates were downloaded from UCSC Genome browser for the mouse (mm9) gene list. BED file of regions of interest were created and defined as coordinates from TSS(-2000bp) to TES, for each gene. Once peaks were obtained for all the tracks, we selected regions of interest for the genes that overlapped with these peaks, with the BEDTOOLS intersect command.
Differentially enriched genes were identified using the DEseq package from Bioconductor using (FDR < 0.1) and the ngs.plot program was used to visualize H3K79me2 and H3K79me3 marks across the genebody.
Genome_build: mm9
Supplementary_files_format_and_content: Table containing ChIP-seq data (raw counts, not normalized) with read counts per each gene from the Transcription start site (-2000bp) to the Transcription End Site for each mutant and wildtype for both H3K79me2 and H3K79me3.
 
Submission date Dec 19, 2014
Last update date May 15, 2019
Contact name John H Bushweller
E-mail(s) jhb4v@virginia.edu
Organization name University of Virginia
Department Molecular Physiology and Biological Physics
Street address 1340 Jefferson Park Avenue
City Charlottesville
State/province VA
ZIP/Postal code 22908
Country USA
 
Platform ID GPL16417
Series (1)
GSE64365 Degree of Recruitment of DOT1L to MLL-AF9 Defines Level of H3K79 Di- and Tri-methylation on Target Genes and Transformation Potential
Relations
BioSample SAMN03269156
SRA SRX818463

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap