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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 13, 2024 |
| Title |
Biochemical properties of chromatin domains define genome compartmentalization [III] |
| Organism |
Mus musculus |
| Experiment type |
Other
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| Summary |
Chromatin three-dimensional (3D) organization inside the cell nucleus determines the separation of euchromatin and heterochromatin domains. Their segregation results in the definition of active and inactive chromatin compartments, whereby the local concentration of associated proteins, RNA and DNA results in the formation of distinct subnuclear structures. Thus, chromatin domains spatially confined in a specific 3D nuclear compartment are expected to share similar epigenetic features and biochemical properties, in terms of accessibility and solubility. Based on this rationale, we developed the 4f-SAMMY-seq to map euchromatin and heterochromatin based on their accessibility and solubility, starting from as little as 10,000 cells. Adopting a tailored bioinformatic data analysis approach we reconstruct also their 3D segregation in active and inactive chromatin compartments and sub-compartments, thus recapitulating the characteristic properties of distinct chromatin states. A key novelty of the new method is the capability to map both the linear segmentation of open and closed chromatin domains, as well as their 3D compartmentalization in one single experiment.
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| Overall design |
SAMMY-seq analysis on mouse C2C12 myoblasts cell line using the 4fraction protocol (4f-SAMMY-seq), two replicates on 2M cells
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| Contributor(s) |
Lucini F, Petrini C, Salviato E, Pal K, Rosti V, Gorini F, Santarelli P, Quadri R, Lembo G, Graziano G, Di Patrizio Soldateschi E, Tagliaferri I, Pinatel E, Sebastyén E, Rotta L, Gentile F, Vaira V, Lanzuolo C, Ferrari F |
| Citation(s) |
38808669 |
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| Submission date |
Mar 21, 2024 |
| Last update date |
Aug 08, 2024 |
| Contact name |
Chiara Lanzuolo |
| E-mail(s) |
lanzuolo@ingm.org
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| Phone |
0200660358
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| Organization name |
CNR and Istituto Nazionale Genetica Molecolare
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| Lab |
Lanzuolo Lab
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| Street address |
Via Francesco Sforza 35
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| City |
Milan |
| State/province |
--- |
| ZIP/Postal code |
20122 |
| Country |
Italy |
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| Platforms (1) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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| Samples (8)
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| GSM8157583 |
2M-rep1, C2C12, S4 |
| GSM8157584 |
2M-rep2, C2C12, S2L |
| GSM8157585 |
2M-rep2, C2C12, S2S |
| GSM8157586 |
2M-rep2, C2C12, S3 |
| GSM8157587 |
2M-rep2, C2C12, S4 |
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| This SubSeries is part of SuperSeries: |
| GSE262104 |
Biochemical properties of chromatin domains define genome compartmentalization |
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| Relations |
| BioProject |
PRJNA1090326 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE262103_RAW.tar |
1.1 Gb |
(http)(custom) |
TAR (of BW) |
SRA Run Selector |
| Raw data are available in SRA |
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