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Series GSE122958 Query DataSets for GSE122958
Status Public on Nov 27, 2018
Title Hi-C contact map of the Jurkat T cell genome
Organism Homo sapiens
Experiment type Other
Summary We performed Hi-C on untreated Jurkat T cells growing in culture. We obtained contact maps with a final resolution of 5 kb where Topologically Associated Domains (TADs) are clearly visible. We identified 3D sub-compartments, characterized by enriched Hi-C contacts within themselves compared to contacts with other compartments. Our results suggest that the A compartment, associated with ongoing transcription, consists of two distinct sub-compartments called A1 and A2; and that the B compartment, associated with lack of transcription, consists of three sub-compartments called B1, B2 and B3. Genes in the A1 and A2 compartments are typically expressed at the same level, but chromatin marks associated with transcription, such as H3K4me2 or H3K27ac, are typically more abundant in A1 than in A2. The B1, B2 and B3 sub-compartments correspond to Polycomb, HP1 and lamina-associated chromatin, which were previously identified types of silent chromatin. Overall, these results suggest that spatial neighborhoods of the Jurkat nucleus correspond to homogeneous chromatin types, and that transcriptionally active regions are in fact two distinct types.
Overall design Two Hi-C libraries were prepared from independent Jurkat T cell cultures.
Contributor(s) Chen H, Zorita E, Stadhouders R, Filion GJ
Citation(s) 31492853
Submission date Nov 26, 2018
Last update date Sep 11, 2019
Contact name Guillaume Filion
Organization name CRG
Department GRSCC
Lab Genome Architecture
Street address Dr. Aiguader 88
City Barcelona
ZIP/Postal code 08003
Country Spain
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (2)
GSM3489136 C029: Jurkat Hi-C
GSM3489137 C034: Jurkat Hi-C
BioProject PRJNA506997
SRA SRP170743

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Supplementary file Size Download File type/resource
GSE122958_jurkat_wt_cluster.txt.gz 1.2 Mb (ftp)(http) TXT 1.7 Gb (ftp)(http) COOL
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