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Series GSE89112 Query DataSets for GSE89112
Status Public on Jan 11, 2017
Title Sub-kilobase resolution Kc167 cell Hi-C
Organism Drosophila melanogaster
Experiment type Other
Summary The locations of chromatin loops in Drosophila were determined by Hi-C (chemical cross-linking, restriction digestion, ligation, and high-throughput DNA sequencing). Whereas most loop boundaries or “anchors” are associated with CTFC protein in mammals, loop anchors in Drosophila were found most often in association with the polycomb group (PcG) protein Polycomb (Pc), a subunit of Polycomb Repressive Complex 1 (PRC1). Loops were frequently located within domains of PcG-repressed chromatin. Promoters located at PRC1 loop anchors regulate some of the most important developmental genes and are less likely to be expressed than those not at PRC1 loop anchors. Although DNA looping has most commonly been associated with enhancer-promoter communication, our results indicate that loops are also associated with gene repression.
 
Overall design Hi-C experiments where ligation is performed on beads (tethered) on embryonic Kc167 Drosophila cultured cells from two independent biological replicates.
 
Contributor(s) Eagen KP, Kornberg RD
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Oct 24, 2016
Last update date May 15, 2019
Contact name Kyle Eagen
E-mail(s) eagen@northwestern.edu
Organization name Northwestern University
Department Biochemistry and Molecular Genetics
Lab Eagen
Street address 303 E Superior St, SQ 7-405
City Chicago
State/province IL
ZIP/Postal code 60611
Country USA
 
Platforms (1)
GPL19132 Illumina NextSeq 500 (Drosophila melanogaster)
Samples (2)
GSM2358971 Kc167_Hi-C_primary
GSM2358972 Kc167_Hi-C_replicate
Relations
BioProject PRJNA350309
SRA SRP091997

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
GSE89112_Kc167combined.hic 1.7 Gb (ftp)(http) HIC
GSE89112_Kc167combined_TADs.txt.gz 105.5 Kb (ftp)(http) TXT
GSE89112_Kc167combined_loops.txt.gz 1.7 Kb (ftp)(http) TXT
GSE89112_Kc167combined_randomized.hic 1.8 Gb (ftp)(http) HIC
GSE89112_RAW.tar 4.4 Gb (http)(custom) TAR (of HIC)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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