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Status |
Public on Oct 14, 2019 |
Title |
Dmel_Hi-C |
Sample type |
SRA |
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Source name |
stage 15-16 embryos
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Organism |
Drosophila melanogaster |
Characteristics |
strain: w1118 Oregon R developmental stage: stage 15-16 embryos tissue: embryos
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Growth protocol |
D. melanogaster and D. virilis flies were maintained in standard Drosophila medium. D. busckii flies were additionally fed with instant Drosophila medium (Formula 4-24, Carolina Biological Supply Company, catalog number 173202) mixed with instant potato powder on top of the standard Drosophila medium.
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Extracted molecule |
genomic DNA |
Extraction protocol |
In situ Hi-C experiments were performed using a modified version of the in situ Hi-C protocol (Rao et al. 2014) described in (Ramirez et al. 2018). Nuclei were extracted by resuspension in 1 mL ice-cold lysis buffer (10 mM Tris-HCl, pH 8, 10 mM NaCl, 0.2% IGEPAL CA-630) and sonication following the standardized nuclear extraction NEXON protocol (Arrigoni et al. 2015) (Covaris E220 sonicator, settings: 75 W peak power, 2 % duty factor, 200 cycles/burst, for 15-30 sec until about 70 % of intact nuclei were released). Samples were filtered through a 30 µm filter to remove bigger embryo fragments. From this step on we followed the protocol described in (Ramirez et al. 2018). Nuclei were digested using DpnII (NEB, R0543M, 150 U/ sample). NEB Next Ultra II
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Library strategy |
Hi-C |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina HiSeq 3000 |
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Description |
SRR7029390,SRR7029389,SRR7029392,SRR7029391 (merge of 2 replicates, each sequenced two-times) processed Hi-C matrices and TAD boundaries.
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Data processing |
Hi-C: Paired-end reads were mapped using bwa mem with parameters -A1 -B4 -E50 -L0 (which promote a read to be split instead of adding a gap) and Hi-C matrices generated using `hicBuildMatrix`, Hi-C matrices of replicates were merged using `hicSumMatrices` and corrected at restriction enzyme resolution using `hicCorrectMatrix` tools from HiCExplorer v1.8.1. TAD boundaries were called using the `hicFindTADs` tool from HiCExplorer with settings `--minDepth 15000 --maxDepth 50000 --step 2000 --thresholdComparisons 0.01 --correctForMultipleTesting bonferroni`. Genome_build: Dvir_HiC, Dbus_HiC, Dm6 Supplementary_files_format_and_content: Hi-C: h5 files of corrected Hi-C matrices of merged two replicates and bed files of TAD boundaries.
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Submission date |
Oct 02, 2018 |
Last update date |
Oct 14, 2019 |
Contact name |
Asifa Akhtar |
E-mail(s) |
akhtarlab_data@ie-freiburg.mpg.de
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Organization name |
Max Planck Institute of Immunobiology and Epigenetics
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Department |
Chromatin Regulation
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Lab |
Akhtar Lab
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Street address |
Stuebeweg 51
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City |
Freiburg |
ZIP/Postal code |
79108 |
Country |
Germany |
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Platform ID |
GPL23323 |
Series (2) |
GSE120751 |
Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling [HiC] |
GSE120752 |
Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling |
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Relations |
BioSample |
SAMN08947962 |
SRA |
SRX3961629 |
SRA |
SRX3961628 |
SRA |
SRX3961627 |
SRA |
SRX3961626 |
Supplementary file |
Size |
Download |
File type/resource |
GSM3414719_Dmel_Hi-C_corrected.h5 |
243.7 Mb |
(ftp)(http) |
H5 |
GSM3414719_Dmel_boundaries.bed.gz |
41.9 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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