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Sample GSM1167158 Query DataSets for GSM1167158
Status Public on Sep 27, 2013
Title H2Aub1 WT
Sample type SRA
Source name CD43 negative mouse resting B cells
Organism Mus musculus
Characteristics strain background: mixed
genotype/variation: wild-type (Cre-ERt2 homozygous)
developmental stage: adult
tissue of origin: spleen
cell type: CD43 negative mouse resting B cells
chip antibody: H2AK119ubq (05-678)
chip antibody vendor: Millipore
chip antibody cat. #: 05-678
Treatment protocol 48 hours incubation with 4-hydroxytamoxifen for samples labeled WT or KO
Growth protocol RPMI, 15% foetal calf serum, 0.1 U/mL penicillin, 0.1 μg/mL streptomycin, 2 mM L-Glutamine, 50 μM beta-mercaptoethanol, 6 ng/ml IL-4
Extracted molecule genomic DNA
Extraction protocol Cells were fixed with 1% formaldehyde and isolated nuclei were sonicated to the desired fragment size. For H2Aubq in wild-type and Aurkb KO cells, unfixed chromatin was prepared from isolated nuclei digested with Micrococcal Nuclease to di-/mono-nucleosome. Pre-coupled antibodies-beads were used to immunoprecipitated chromatin bound proteins/histone marks. After DNA purification, a total of 10 ng immunoprecipitated input was used for the library preparation with NEBNext ChIP-seq Library Prep Master Mix Set for Illumina (NEB) and Multiplexing Sample Preparation Oligonucleotide Kit (Illumina)
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
Description Homozygous Rosa26-CreERT2 treated for 48 hours with 250 nM 4-hydroxytamoxifen
Data processing The reads were aligned to Mouse genome mm9 using Bowtie version 0.12.8 using '-S -n 2 -l 25 -m 1' parameters. Only reads aligned uniquely to the genome were retained for further analysis.
Reads with identical chromosomal co-ordinates and orientation (duplicates) were filtered using Picard version 1.65
To visualise the genomic coverage of samples in UCSC genome browser, the reads were extended to estimated fragment size and converted to BigWig format. The fragment size was estimated using SISSR method (Jothi et al., 2008)
Genome_build: mm9
Supplementary_files_format_and_content: BigWig
Submission date Jun 18, 2013
Last update date May 15, 2019
Contact name Gopuraja Dharmalingam
Organization name MRC London Institute of Medical Sciences
Department Epigenetics section
Street address Faculty of Medicine, Imperial College, Hammersmith Hospital Campus
City London
ZIP/Postal code W12 0NN
Country United Kingdom
Platform ID GPL13112
Series (2)
GSE42705 The Aurora B kinase and the polycomb protein Ring1B combine to regulate active promoters in quiescent lymphocytes [ChIP-seq]
GSE42706 The Aurora B kinase and the polycomb protein Ring1B combine to regulate active promoters in quiescent lymphocytes
BioSample SAMN02207413
SRA SRX309667

Supplementary file Size Download File type/resource 349.8 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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