 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jul 16, 2012 |
| Title |
OCI-Ly1-H3K4me3-ChIPseq |
| Sample type |
SRA |
| |
|
| Source name |
Diffuse Large B-cell Lymophoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: OCI-Ly1
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 |
LY1_H3K4me3May09Feb10_BWA.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 |
| E-mail(s) |
yaj2001@med.cornell.edu
|
| 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 |
|
| Relations |
| SRA |
SRX110935 |
| BioSample |
SAMN00765035 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM847242_LY1_H3K4me3May09Feb10_BWA.SNVs.dbSNP.annot.1KG.kmut.TFBS.cons.flseq.qs.txt.gz |
3.0 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
