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Sample GSM847244 Query DataSets for GSM847244
Status Public on Jul 16, 2012
Title NBC-H3K4me3-ChIPseq
Sample type SRA
Source name Human tonsilar naïve B cells
Organism Homo sapiens
Characteristics cell type: Human tonsilar naïve B cells (IgD+)
chip antibody: H3K4me3
Treatment protocol Primary cells were purified from normal fresh human tonsillectomy specimens by magnetic cell separation based on the expression of phenotypic markers, such as IgD for Naïve B cells, and CD77 for germinal center B cells. These human tissues were obtained with the approval of the Institutional Review Boards of the Weill Cornell Medical College in accordance with the Declaration of Helsinki. Ficoll Histopaque gradient centrifugation was used to isolate tonsilar mononuclear cells. Individual tonsilar B cell populations were collected by antibody-based microbead cell separation (Miltenyi Biotec, Auburn, CA). The purity of the isolated cells is normally more than 90%.
Growth protocol The OCI-Ly1 cells were cultured in medium containing 90% Iscove medium (Cellgro, Manassas, VA), 10% fetal bovine serum (Gemini, Irvine, CA), and 1% penicillin/streptomycin (Invitrogen, Carlsbad, CA). The OCI-Ly8 cells were grown in RPMI with 10% fetal calf serum, 1% penicillin/streptomycin, and N-2-hydroxyethylpiperazine-N′-2-ethanesulfonic acid.
Extracted molecule genomic DNA
Extraction protocol Sequencing libraries were constructed from 10ng ChIP or Input DNA following Illumina protocol. Fragments between 200bp to 300bp in size were selected. 7 pM of final library product was sequenced either on GAIIX or HiSeq2000.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
Data processing NB062510_H3K4me3_Run083010_s_5_sequence.txt.gz.sam.SNVs.dbSNP.annot.1KG.kmut.TFBS.Cons.flseq.qs; genome build: hg18
After sequencing, short reads were aligned to the human genome (hg18) using the BWA short read aligner. We then detected single nucleotide variants (SNVs) by using an algorithm, SHMseeqer, developed in house. After eliminating known dbSNPs and low confidence novel SNVs, SHMseeqer searches for SNVs that occur at dC or dG within the WRCY or the RGYW motif, which represent the features of somatic hypermutaiton. SHMseeqers then calculates Z-scores to measure the over-representation of SHMs in SNVs at a 4-kb window centered at the transcription starting site (TSS) of each RefSeq gene. Any promoters with 3 and more SHMs and a Z-score greater than 1 will be defined as SHM hotspots.
Submission date Dec 09, 2011
Last update date May 15, 2019
Contact name Yanwen Jiang
Organization name Weill Cornell Medical College
Street address 413 E. 69th St. BB1462
City New York
State/province NY
ZIP/Postal code 10021
Country USA
Platform ID GPL10999
Series (1)
GSE34316 Genome-wide Detection of Genes Targeted by Aberrant Somatic Hypermutation in Lymphoma
SRA SRX110937
BioSample SAMN00765037

Supplementary file Size Download File type/resource
GSM847244_NB062510_H3K4me3_Run083010.SNVs.dbSNP.annot.1KG.kmut.TFBS.Cons.flseq.qs.txt.gz 2.6 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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