|
| Status |
Public on Jun 02, 2016 |
| Title |
Jmjd2c_Ctrl |
| Sample type |
SRA |
| |
|
| Source name |
L-GMP transformed with MLL-AF9
|
| Organism |
Mus musculus |
| Characteristics |
cell type: L-GMP transformed with MLL-AF9
genotype: Jmjd2a/b/cf/f;Rosa26::CreERT2
strain background: C57BL/6
chip antibody: anti-Jmjd2c, ktwl
|
| Treatment protocol |
To induce knockout cells were grown in the presence of 500nM OHT 4-hydroxytamoxifen for 96hr.
|
| Growth protocol |
Cells were grown in RPMI containing 20% FBS and 10ng/ml IL-3
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIPSeq libraries were made using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® according to the manufactures protocol
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
ChIPSeq reads were aligned to the mm10 genome assembly using bowtie (Version 0.12.7) with the following settings: -q -p 4 -S -n 2 -e 70 -l 28 --maxbts 800 -k 1 -a -m 1 --best --strata --phred33-quals.
Mapped reads were filtered for PCR dublicates using 'samtools rmdup' (Version 0.1.19) and coverted to bed format with 'bedtools bamtobed' (Version 2.25.0)
Peaks were called in Jmjda and Jmjd2c data set for Ctrl vs OHT, using EaSeq (Version 1.0) with the following settings: for Jmjd2a fold difference above 1, for Jmjd2c fold difference above 3.
Peak annotation was based on RefSeq database annotation (UCSC refFlat, mm10 genome assembly, 19 January 2015).
Genome_build: mm10
Supplementary_files_format_and_content: text files with called peaks for anti-Jmjd2a and anti-Jmjd2c. Bigwig files of genome-wide read coverage are available for all samples.
|
| |
|
| Submission date |
May 10, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Karl Agger |
| E-mail(s) |
karl.agger@bric.ku.dk
|
| Phone |
+4522832639
|
| Organization name |
University of Copenhagen
|
| Department |
BRIC
|
| Street address |
Ole Maaloes Vej 5
|
| City |
Copenhagen |
| ZIP/Postal code |
2200 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE81299 |
Identification of Kdm4a and c target genes in MLL-AF9 transformed mouse GMPs (L-GMP) [ChIP-seq] |
| GSE81300 |
Identification of Kdm4a, b and c target genes in MLL-AF9 transformed mouse GMPs (L-GMP) |
|
| Relations |
| BioSample |
SAMN04977961 |
| SRA |
SRX1755829 |
