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Series GSE31105 Query DataSets for GSE31105
Status Public on Oct 10, 2011
Title Chromatin Conformation Capture in two biological replicates of K562 cells to identify interactions between tRNA genes in human cells.
Organism Homo sapiens
Experiment type Other
Summary tRNA genes are believed to form clusters in three-dimensional space in smaller eukaryotes (yeasts). In the course of investigating a cluster of tRNA genes for insulator activity in humans, we addressed whether these tRNA genes clustered with other tRNA genes. We used an anchor point to generate 4C material from a tRNA cluster located on chromosome 17 (hg18 7.962400 MB). We identify interactions occurring within the 300kb region of this point, but only extending in one direction and suggesting these interactions occur between this tRNA cluster and other tRNA gene clusters from this locus. We did not observed any specific interactions outside of this region or on other chromsomes, perhaps due to an low number of mappable reads from our samples.
 
Overall design Chromatin Conformation Capture in two biological replicates of K562 cells to identify interactions between tRNA genes in human cells.
 
Contributor(s) Raab J, Katzman S, Kamakaka R
Citation(s) 22085927
Submission date Aug 01, 2011
Last update date May 15, 2019
Contact name Jesse Raab
Organization name UC Santa Cruz
Department MCD Biology
Lab Rohinton Kamakaka
Street address 1156 High St
City Santa Cruz
State/province CA
ZIP/Postal code 95064
Country USA
 
Platforms (1)
GPL9052 Illumina Genome Analyzer (Homo sapiens)
Samples (2)
GSM770072 K562_rep1
GSM770073 K562_rep2
Relations
SRA SRP007635
BioProject PRJNA144669

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
GSE31105_RAW.tar 2.6 Mb (http)(custom) TAR (of BAM, BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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