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Sample GSM1048205 Query DataSets for GSM1048205
Status Public on Sep 27, 2013
Title Aurora B
Sample type SRA
Source name CD43 negative mouse resting B cells
Organism Mus musculus
Characteristics strain background: C57BL/6
genotype/variation: wild-type
developmental stage: adult
tissue: spleen
chip antibody info.: Aurora B (ab2254), Abcam
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. Pre-coupled antibodies-beads were used to immunoprecipitated chromatin bound proteins/histone marks. After cross-link reversal and 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 Wild-type
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)
Aurkb binding regions were identified using MACS2 with default parameters (MACS2_Peaks_GEO.xlsx)
Genome_build: mm9
Supplementary_files_format_and_content: BigWig
Supplementary_files_format_and_content: 'MACS2_Peaks_GEO.xlsx' peak file
Submission date Dec 04, 2012
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
SRA SRX208207
BioSample SAMN01822805

Supplementary file Size Download File type/resource 271.8 Mb (ftp)(http) BW
GSM1048205_MACS2_Peaks_GEO.xlsx.gz 303.8 Kb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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