|
| Status |
Public on Apr 30, 2015 |
| Title |
D546R_H3K79me3 |
| Sample type |
SRA |
| |
|
| Source name |
Hematopoietic progenitor cells
|
| Organism |
Mus musculus |
| Characteristics |
cell-type: Primary Hematopoietic progenitor cells
genotype/variation: MLL-AF9 (D546R)
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 |
SAMN03269158 |
| SRA |
SRX818464 |
