GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM2814007 Query DataSets for GSM2814007
Status Public on Mar 28, 2019
Title ChIPseq mouse LUC/LUC#2-H3K4me3
Sample type SRA
Source name NIH/3T3 tet-on 3G cells
Organism Mus musculus
Characteristics cell line: 3T3
antibody: Histone H3 trimethyl Lys4 antibody (Millipore, cat no. 17-614)
Extracted molecule genomic DNA
Extraction protocol Libraries were prepared according to Illumina's instructions. The ChIP DNA ends were repaired using PNK and Klenow enzyme, followed by treatment with Taq polymerase to generate a protruding 3 A base used for adaptor ligation. Following ligation of a pair of Solexa adaptors to the repaired ends, the ChIP DNA was amplified using the adaptor primers for 17 cycles and the fragments around 220 bp (mononucleosome + adaptors) isolated from agarose gel. Libraries were sequenced on the Hi-seq following the manufacturer's protocols. As described in Barski et al., 2007 (A. Barski, S. Cuddapah, K. Cui, T.Y. Roh, D.E. Schones, Z. Wang, G. Wei, I. Chepelev and K. Zhao, High-resolution profiling of histone methylations in the human genome, Cell 129 (2007), pp. 823-837).
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
Data processing Basecalls performed using RTA 1.7 or Illumina Casava1.7
ChIP-seq reads were mapped to the mouse genome (mm9) using Bowtie2. The reads with MAPQ <=10 or redundant reads were removed for further analysis in each library.
We identified Enriched-ChIP regions using SLICER
Genome_build: mm9
Supplementary_files_format_and_content: txt: plan text file. Each line is a peak region. The five columns are chrom, chrom_index, start position, end position, peak position.
Submission date Oct 16, 2017
Last update date Mar 29, 2019
Contact name Keji Zhao
Organization name national Institute of Health
Department National Heart, Lung, and Blood Institute
Street address Building 10 Room 7B06A
City Bethesda
State/province MD
ZIP/Postal code 20814
Country USA
Platform ID GPL13112
Series (1)
GSE105012 Single cell chromatin immunocleavage sequencing (scChIC-Seq) to profile histone modification
BioSample SAMN07789043
SRA SRX3287557

Supplementary file Size Download File type/resource
GSM2814007_KZ730-GA6909_0_0_mapq10_noDup-W200-G200-E.01_S100_with_peak_pos_sorted.txt.gz 167.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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