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| Status |
Public on Nov 16, 2016 |
| Title |
DpnII_HiC |
| Sample type |
SRA |
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| Source name |
Kc167 _DpnII
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| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: Kc167
cell type: Drosophila Embryonic Cell Line
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were crosslinked with 1% formaldehyde for 10 min at room temperature and quenched with glycine. Nuclear lysates were digested with DpnII or Hinf1 and fragment ends were filled with biotinylated nucleotides prior to ligatation. Ligated fragments were reverse crosslinked, purified, and sonicated prior to generation of Illumina libraries.
Libraries were constructed using the standard protocol. Genomic fragments were end repaired (NEBNext End Repair Module), A-tailed by adding adenosine to the 3’ ends of fragment using Klenow fragment (3’ to 5’ exo minus, New England Biolabs), and adaptors were ligated at room temperature for 1 hr with T4 DNA ligase (New England Biolabs). Libraries were amplified with Illumina primers using the KAPA SYBR FAST qPCR Master Mix.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
HiC Library digested with DpnII
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| Data processing |
Library strategy: Hi-C
Raw HiC data from this submission and the four normal temperature HiC biological replicates digested with DpnII from GSE63515 (GSM1551441, GSM1551442, GSM1551443, GSM1551444) were combined and processed through the Juicer pipeline (Rao et al. 2014. Cell. 159:1665-80) to generate the .hic file.
To identify the significant genomic interactions, the .hic file was further processed through ICE and Fit-Hi-C (Imakaev, et al. 2012. Nature. 9:999-1003; Ay et al. 2014. Genome Research. 24:999-1011)
Genome_build: dm6
Supplementary_files_format_and_content: The .hic file contains the HiC contact matrix. The Fithic .txt file contains the genomic coordinates of the interactions anchors in columns 1-3 and 4-6. The p value and q value for each interaction are reported in column 7 and 8, respectively.
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| Submission date |
Apr 26, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Victor G Corces |
| E-mail(s) |
vcorces@emory.edu
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| Phone |
4047274250
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| Organization name |
Emory University
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| Department |
Biology
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| Lab |
Corces Lab
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| Street address |
1510 Clifton Rd
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| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30322 |
| Country |
USA |
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| Platform ID |
GPL13304 |
| Series (2) |
| GSE80701 |
Distinct Enhancer Classes in Drosophila Bind Different Architectural Proteins and Mediate Unique Chromatin Interactions and 3D Architecture [Hi-C] |
| GSE80702 |
Different Enhancer Classes in Drosophila Bind Different Architectural Proteins and Mediate Unique Chromatin Interactions and 3D Architecture |
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| Relations |
| BioSample |
SAMN04903889 |
| SRA |
SRX1728721 |
| 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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