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Sample GSM3414719 Query DataSets for GSM3414719
Status Public on Oct 14, 2019
Title Dmel_Hi-C
Sample type SRA
 
Source name stage 15-16 embryos
Organism Drosophila melanogaster
Characteristics strain: w1118 Oregon R
developmental stage: stage 15-16 embryos
tissue: embryos
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.
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
 
Library strategy Hi-C
Library source genomic
Library selection other
Instrument model Illumina HiSeq 3000
 
Description SRR7029390,SRR7029389,SRR7029392,SRR7029391 (merge of 2 replicates, each sequenced two-times)
processed Hi-C matrices and TAD boundaries.
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.
 
Submission date Oct 02, 2018
Last update date Oct 14, 2019
Contact name Asifa Akhtar
E-mail(s) akhtarlab_data@ie-freiburg.mpg.de
Organization name Max Planck Institute of Immunobiology and Epigenetics
Department Chromatin Regulation
Lab Akhtar Lab
Street address Stuebeweg 51
City Freiburg
ZIP/Postal code 79108
Country Germany
 
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
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 SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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