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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 05, 2018 |
| Title |
Kieffer-Kwon-2017-HIC053 |
| Sample type |
SRA |
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| Source name |
B cells
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL6/J
genotype: Mycflox/flox-CRE
tissue: spleen
activation time: 24h
tissue: spleen
cell type: splenic B cells isolated from 6-8 weeks old RosaCreERTam/Myc flox/flox mouse spleen by negative selection
protocol: in situ Hi-C
treatment: mice were treated with tamoxifen (three times of i.p. 1mg/mouse at 4, 3 and 1 day before sacrifice); B cells were activated for 24 hours with LPS (50 μg/mL; Sigma), IL-4 (2.5 ng/mL; Sigma), and anti-CD180 (RP105) antibody (0.5 μg/mL, BD PharMingen)
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| Treatment protocol |
treatment protocol for specific samples are specified in the SAMPLES section
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| Growth protocol |
specificed in the SAMPLES section
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were crosslinked and then lysed with nuclei permeabilized but still intact. DNA was then restricted and the overhangs filled in incorporating a biotinylated base. Free ends were then ligated together in situ. Crosslinks were reversed, the DNA was sheared to 300-500bp and then biotinylated ligation junctions were recovered with streptavidin beads.
standard Illumina library construction protocol, Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 8-12 cycles and library fragments of 400-600 bp (insert plus adaptor and PCR primer sequences) were purified using SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeqX Ten, or HiSeq 2500 following the manufacturer's protocols
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
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| Data processing |
The paired end reads were aligned separately using BWA against the mm9 mouse build
PCR duplicates, low mapping quality and unligated reads were removed using Juicer (see Rao, Huntley, et al Cell 2014; Durand, Shamim, et al Cell Systems 2016)
Contact matrices were constructed at various resolutions and normalized using Juicer (see Rao, Huntley, et al Cell 2014; Durand, Shamim, et al Cell Systems 2016)
loops were annotated using HiCCUPS (see Rao, Huntley, et al Cell 2014; Durand, Shamim, et al Cell Systems 2016), domains were annotated using Arrowhead (see Rao, Huntley, et al Cell 2014; Durand, Shamim, et al Cell Systems 2016)
Genome_build: mm9 (mouse)
Supplementary_files_format_and_content: .hic file (contains contact matrices at various resolutions in an easy to visualize and access format) (see Durand, Robinson, et al Cell Systems 2016)
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| Submission date |
May 04, 2018 |
| Last update date |
May 09, 2019 |
| Contact name |
Seolkyoung Jung |
| Organization name |
NIH
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| Department |
NIAMS
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| Lab |
biodata mining and discovery section
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| Street address |
10 Center Dr
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| City |
bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL21273 |
| Series (1) |
| GSE82144 |
Myc regulates chromatin decompaction and nuclear architecture during B cell activation |
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| Relations |
| BioSample |
SAMN09076506 |
| SRA |
SRX4044200 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3131766_Kieffer-Kwon-2017-HIC053.hic |
1.4 Gb |
(ftp)(http) |
HIC |
| GSM3131766_Kieffer-Kwon-2017-HIC053_30.hic |
1.4 Gb |
(ftp)(http) |
HIC |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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