NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1180106 Query DataSets for GSM1180106
Status Public on Jul 04, 2013
Title mouse/plasmacytoma PCT4961/H2BK120Ac/rep1
Sample type SRA
 
Source name mouse plasmacytoma PCT4961
Organism Mus musculus
Characteristics antibody: H2BK120Ac
cell type: plasmacytoma PCT4961
strain: Balb/c
genotype: AID-/- BclXL
Extracted molecule genomic DNA
Extraction protocol Cells were fixed with 1% paraformaldehyde at 37C for 10 minutes followed by quenching with glycine and sonnication. Chromatin fragments were then immunoprecipitated with an anti-H2BK120Ac antibody following standard protocols. Immunoprecipitates were processed according to Illumina's standard protocol
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
 
Data processing Image analysis, base calling, quality filtering: Standard settings of GAPipeline using PhiX control; ***Raw data***: Fastq files contain full length reads that passed the chastity filter. Qualities were scaled to phred33 format for all files. ***Wig file***: Reads were aligned to the mouse genome (build mm9) with bowtie accepting only reads that had a unique match in the genome in their top quality stratum (bowtie 0.12.8, --best --all --strata -m1 -n2 -l50). Redundancy was capped at a maximum of 3 identically aligned reads, and reads shifted by half the approximate fragment size of 120 towards the fragment center were counted in 100 nt bins along the genome. Counts were normalized to the non redundant library size and bin size such that the final units are reads per kb per million (RPKM).
 
Submission date Jul 03, 2013
Last update date May 15, 2019
Contact name Seolkyoung Jung
Organization name NIH
Department NIAMS
Lab biodata mining and discovery section
Street address 10 Center Dr
City bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL11002
Series (1)
GSE48514 A mouse model of endemic Burkitt translocations reveals the long-range boundaries of Ig-mediated oncogene deregulation
Relations
BioSample SAMN02225372
SRA SRX317629

Supplementary file Size Download File type/resource
GSM1180106_r090916B_l4_PCT4961_nd_H2BK120Ac.wig.gz 17.6 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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