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| Status |
Public on Nov 27, 2018 |
| Title |
Hi-C contact map of the Jurkat T cell genome |
| Organism |
Homo sapiens |
| Experiment type |
Other
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| 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.
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| Overall design |
Two Hi-C libraries were prepared from independent Jurkat T cell cultures.
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| Contributor(s) |
Chen H, Zorita E, Stadhouders R, Filion GJ |
| Citation(s) |
31492853 |
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| Submission date |
Nov 26, 2018 |
| Last update date |
Sep 11, 2019 |
| Contact name |
Guillaume Filion |
| E-mail(s) |
guillaume.filion@gmail.com
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| Organization name |
CRG
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| Department |
GRSCC
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| Lab |
Genome Architecture
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| Street address |
Dr. Aiguader 88
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| City |
Barcelona |
| ZIP/Postal code |
08003 |
| Country |
Spain |
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| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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| Samples (2) |
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| Relations |
| BioProject |
PRJNA506997 |
| SRA |
SRP170743 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE122958_jurkat_wt_cluster.txt.gz |
1.2 Mb |
(ftp)(http) |
TXT |
| GSE122958_jurkat_wt_hg19_5k_q10.cool.gz |
1.7 Gb |
(ftp)(http) |
COOL |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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