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| Status |
Public on Mar 28, 2019 |
| Title |
ChIPseq mouse LUC/LUC#2-H3K4me3 |
| Sample type |
SRA |
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| Source name |
NIH/3T3 tet-on 3G cells
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| Organism |
Mus musculus |
| Characteristics |
cell line: 3T3
antibody: Histone H3 trimethyl Lys4 antibody (Millipore, cat no. 17-614)
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| 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).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| 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.
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| Submission date |
Oct 16, 2017 |
| Last update date |
Mar 29, 2019 |
| Contact name |
Keji Zhao |
| E-mail(s) |
zhaok@nhlbi.nih.gov
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| Organization name |
national Institute of Health
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| Department |
National Heart, Lung, and Blood Institute
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| Street address |
Building 10 Room 7B06A
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20814 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE105012 |
Single cell chromatin immunocleavage sequencing (scChIC-Seq) to profile histone modification |
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| Relations |
| 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 Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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