NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1296633 Query DataSets for GSM1296633
Status Public on Dec 24, 2013
Title LY1_DMSO_WCE_ChipSeq
Sample type SRA
 
Source name Diffuse Large B-Cell Lymphoma
Organism Homo sapiens
Characteristics chip antibody: None
antibody catalog number: None WCE
cell line: LY1
cell type: Diffuse Large B-Cell Lymphoma
Treatment protocol 0.05% DMSO for 6 hours
Growth protocol RPMI 1640 supplemented with 20% FCS and 1% GlutaMAX.
Extracted molecule genomic DNA
Extraction protocol Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies.
Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description Chromatin IP against LY1_DMSO_WCE
barcode: TTAGGC
Data processing Images analysis and base calling was done using the solexa pipeline.
For samples Colo741_WCE_ChipSeq, Colo741_H3K27ac_ChipSeq, HT29_CDK8_ChipSeq, HT29_WCE_ChipSeq, HT29_H3K27ac_ChipSeq, SW480_WCE_ChipSeq, and SW480_CDK8_ChipSeq reads were aligned to their indicated build using bowtie with parameters -n 2 -e 70 -m 2 -k 2 --best -l 40. Seed length (-l) was set to read length for each dataset.
For samples LY1_WT_WCE_ChipSeq, LY1_JQ1_WCE_ChipSeq, LY1_DMSO_WCE_ChipSeq, LY1_DMSO_BRD4_ChipSeq, LY1_DMSO_POL2_ChipSeq, LY1_JQ1_BRD4_ChipSeq, LY1_WT_MED1_ChipSeq, and LY1_JQ1_POL2_ChipSeq reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.
 
Submission date Dec 23, 2013
Last update date May 15, 2019
Contact name Richard A Young
E-mail(s) young_computation@wi.mit.edu
Phone 617-258-5219
Organization name Whitehead Institute for Biomedical Research
Lab Young Lab
Street address 9 Cambridge Center
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
 
Platform ID GPL11154
Series (1)
GSE53601 ChIP-Seq of Transcriptional Components in Ly1 DLBCL and Colon carcinoma
Relations
BioSample SAMN02485434
SRA SRX398290

Supplementary file Size Download File type/resource
GSM1296633_01182013_C1FJWACXX_2.TTAGGC.wig.gz 19.0 Kb (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