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| Status |
Public on Mar 14, 2018 |
| Title |
18776_WTBM-H4R3_S4_L999_R1_001 |
| Sample type |
SRA |
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| Source name |
Total bone marrow
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| Organism |
Mus musculus |
| Characteristics |
cell source: Total bone marrow
genotype: WT
ChIP: Anti-H4R3me2s, Active Motif Cat#61187
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| Treatment protocol |
Gene-trap knockout
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP on native chromatin from hematopoitic stem/progenitor cells was performed following previously published protocols (M. Girardot et al., 2014. Nucleic acids research 42, 235-248) with the following modifications using ChIP-grade Magna protein A/G beads (Cat#: 16-663, EMB Millipore). The isolated nuclei were incubated for 15 min at 37°C with 4 units/uL of Micrococcal nuclease (M0247, New England Biolabs) to produce mono/di-nucleosomes as verified by agarose gel electrophoresis. Nucleosomes were precipitated with control IgG, ChIP-grade anti-H4R3me2s (Cat#: Ab5823, Abcam) or anti-H3K9me2s (Cat#: 39375, Active motif). ChIP or input DNA was purified with Ampure XP beads (Cat#: A63880, Beckman Coulter).
ChIP libraries were repard according to standard Illumina protocols. Transcriptome libraries were constructed with TruSeq RNA Sample Preparation Kit V2 (Illumia) with minor modifications.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
ChIP-seq: Illumina Casava1.8 software used for basecalling. Reads were aligned to mouse reference genome (mm9) using NovoAlign (http://www.novocraft.com/).
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph
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| Submission date |
Dec 11, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Juan Du |
| Organization name |
Beckman Research Institute, City of Hope
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| Street address |
1500 E. Duarte Rd
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| City |
Duarte |
| State/province |
CA |
| ZIP/Postal code |
91010 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE94966 |
Define roles of JMJD1B in mediating histone demethylation and gene expression |
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| Relations |
| BioSample |
SAMN08161506 |
| SRA |
SRX3462001 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2883924_18776_WTBM-H4R3_S4.bedGraph.gz |
233.1 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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