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| Status |
Public on Aug 08, 2017 |
| Title |
3h LPS RelA ChIP |
| Sample type |
SRA |
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| Source name |
3h LPS RelA
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
cell type: Bone marrow derived macrophages
treatment: 3h LPS RelA
chip antibody: RelA (Ab7970, Abcam) and Dynabeads Protein A
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| Treatment protocol |
Primary macrophages derived from bone marrow were stimulated with lipopolysaccharide and/or Dex for the indicated number of hours.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For RelA ChIP, BMDMs were subject to crosslinking with 1% formaldehyde for 10 minutes at room temperature. For GR ChIP, we used a dual crosslinking method (Uhlenhaut et al., 2013) to detect both tethered and directly bound chromatin. BMDMs were subject to crosslinking with 2mM disuccinimidyl glutarate (DSG) for 30 min followed by 1% formaldehyde for 10 min at room temperature. After crosslinking, chromatin was isolated from about 4 × 10^7 cells, which allows 2 to 3 different immunoprecipitations per sample at a time, and then processed as follows. The lysis buffer to shear the chromatin contained 0.5% SDS, 10 mM EDTA (pH 8), 50 mM tris-HCl (pH 8), and proteinase inhibitor cocktail. Sonication was performed to shear the chromatin to generate DNA fragments with a size range of 400 to 500 base pairs. The sheared chromatin samples were diluted 1:5 in dilution buffer (0.01% SDS, 1.1% Triton-X, 1.2 mM EDTA (pH 8), 20 mM tris-HCl (pH 8), 167 mM NaCl, and proteinase inhibitor cocktail). For each ChIP, 200 µg chromatin DNA was precipitated with antibody coated bead complexes (Dynabeads Protein A for RelA ChIP; anti-IgG paramagnetic beads for GR ChIP, Invitrogen).
sequencing libraries were generated using Illumina TruSeq V3 protocol and subject to 51 bp single-end sequencing on Illumina HiSeq2000.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
GH1397
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| Data processing |
Base-calling with Illumina run time analysis software 1.12.4.2
Alignment to mm9 using Casava Eland extended
ChIP-seq binding sites were identified as hotspots after adjustment using the input DNA control.
Genome_build: mm9
Supplementary_files_format_and_content: BedGraph, csv
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| Submission date |
Jan 17, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Songjoon Baek |
| Organization name |
NCI / NIH
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| Department |
CCR
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| Lab |
LRBGE
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| Street address |
41 Library Drive
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (2) |
| GSE93736 |
Anti-inflammatory Chromatinscape Associated with Clinically Relevant Timing of Glucocorticoid Treatment [ChIP-seq] |
| GSE93739 |
Anti-inflammatory Chromatinscape Associated with Clinically Relevant Timing of Glucocorticoid Treatment |
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| Relations |
| BioSample |
SAMN06236706 |
| SRA |
SRX2498786 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2461325_GH1397_BMDM_RelA_3hLPS_3h_ChIP_mm9_hotspot.csv.gz |
143.8 Kb |
(ftp)(http) |
CSV |
| GSM2461325_GH1397_RelA_BMDM_ChIP_mm9.BEDGRAPH.gz |
119.0 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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