GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE72510 Query DataSets for GSE72510
Status Public on Nov 05, 2015
Title Polytene Hi-C
Organism Drosophila melanogaster
Experiment type Other
Summary Chemical cross-linking and high-throughput sequencing have revealed regions of intra-chromosomal interaction, referred to as topologically associating domains (TADs), interspersed with regions of little or no such interaction, in interphase nuclei. We find that TADs and the regions between them correspond with the bands and interbands of polytene chromosomes of Drosophila. We further establish the conservation of TADs between polytene and diploid cells of Drosophila. From direct measurements on light micrographs of polytene chromosomes, we then deduce the states of chromatin folding in the diploid cell nucleus. Two states of chromatin folding, fully extended fibers containing regulatory regions and promoters, and fibers condensed up to ten-fold containing coding regions of active genes, constitute the euchromatin of the nuclear interior. Chromatin fibers condensed up to 30-fold, containing coding regions of inactive genes, represent the heterochromatin of the nuclear periphery. A convergence of molecular analysis with direct observation thus reveals the architecture of interphase chromosomes.
Overall design Hi-C experiments where ligation is performed on beads (tethered) on male Drosophila salivary glands from three independent biological replicates. Also one Hi-C experiment where the ligation is performed in solution (conventional).
Contributor(s) Eagen KP, Kornberg RD
Citation(s) 26544940
Submission date Aug 28, 2015
Last update date May 15, 2019
Contact name Kyle Eagen
Organization name Baylor College of Medicine
Department Department of Molecular and Cellular Biology
Lab Eagen Lab
Street address 1 Baylor Plaza
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
Platforms (2)
GPL16479 Illumina MiSeq (Drosophila melanogaster)
GPL19132 Illumina NextSeq 500 (Drosophila melanogaster)
Samples (4)
GSM1863750 Polytene_Hi-C_tethered_rep1
GSM1863751 Polytene_Hi-C_tethered_rep2
GSM1863752 Polytene_Hi-C_tethered_rep3
This SubSeries is part of SuperSeries:
GSE72512 Stable Chromosome Condensation Revealed by Chromosome Conformation Capture
BioProject PRJNA294189
SRA SRP062964

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE72510_RAW.tar 24.3 Mb (http)(custom) TAR (of TXT)
GSE72510_tethered_merged_contacts_100kb_bins.txt.gz 7.1 Mb (ftp)(http) TXT
GSE72510_tethered_merged_contacts_15kb_bins.txt.gz 20.3 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap