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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 18, 2018 |
| Title |
Vian-2018-HIC241 |
| Sample type |
SRA |
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| Source name |
activated B cell
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| Organism |
Mus musculus |
| Characteristics |
genotype: WT
cell type: splenic B cells
tissue: spleen
strain: C57BL6/J
age: 6-8 weeks old
protocol: in situ HiC
activation time: activated,24h, oligomycin
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| Treatment protocol |
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); for acute ATP depletion, 20h-activated cells were shifted to glucose deficient media for 2h then, 2-Deoxy-D-glucose (5mM, Sigma) and Oligomycin (126nM, Sigma) were added to the culture for another 1.5-2h before the harvest.
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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, NextSeq 500, 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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| Description |
splenic B cells isolated from 6-8 weeks old C57BL6/J mouse spleen by negative selection
oligomycin treated
Vian-2018-activated_B_cells_24_hours_oligomycin_30.hic
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| Data processing |
The paired end reads were aligned separately using BWA against the mm9 mouse build or the b37 human 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), b37 (human)
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 18, 2018 |
| Last update date |
May 19, 2018 |
| 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) |
| GSE98119 |
The energetics and physiological impact of cohesin extrusion |
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| Relations |
| BioSample |
SAMN09225066 |
| SRA |
SRX4099797 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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