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Series GSE226718 Query DataSets for GSE226718
Status Public on May 13, 2024
Title Biochemical properties of chromatin domains define their compartmentalization [I]
Organism Homo sapiens
Experiment type Other
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.
 
Overall design SAMMY-seq analysis on primary fibroblast cell lines, using two different protocols with three biological replicates each. For the 4-fractions protocol, we performed also replicates on 50k cells and on 10k cells
 
Contributor(s) Lucini F, Petrini C, Salviato E, Pal K, Rosti V, Gorini F, Santarelli P, Quadri R, Di Patrizio Soldateschi E, Lembo G, Tagliaferri I, Pinatel E, SebestyƩn E, Rotta L, Gentile F, Vaira V, Graziano G, Ferrari F, Lanzuolo C
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Submission date Mar 06, 2023
Last update date May 13, 2024
Contact name Chiara Lanzuolo
E-mail(s) lanzuolo@ingm.org
Phone 0200660358
Organization name CNR and Istituto Nazionale Genetica Molecolare
Lab Lanzuolo Lab
Street address Via Francesco Sforza 35
City Milan
State/province ---
ZIP/Postal code 20122
Country Italy
 
Platforms (2)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
GPL30173 NextSeq 2000 (Homo sapiens)
Samples (19)
GSM7082554 C004-r1_4f_S2L
GSM7082555 C004-r1_4f_S2S
GSM7082556 C004-r1_4f_S3
This SubSeries is part of SuperSeries:
GSE262104 Biochemical properties of chromatin domains define genome compartmentalization
Relations
BioProject PRJNA941275

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
GSE226718_C004-r1_10Kh_S2L_R1.bw 186.7 Mb (ftp)(http) BW
GSE226718_C004-r1_10Kh_S2S_R1.bw 189.9 Mb (ftp)(http) BW
GSE226718_C004-r1_10Kh_S3_R1.bw 178.3 Mb (ftp)(http) BW
GSE226718_C004-r1_10Kh_S3vsS2S_R1.bw 533.5 Mb (ftp)(http) BW
GSE226718_C004-r1_10Kh_S4_R1.bw 154.1 Mb (ftp)(http) BW
GSE226718_C004-r1_4f_S2L_R1.bw 185.4 Mb (ftp)(http) BW
GSE226718_C004-r1_4f_S2S_R1.bw 189.2 Mb (ftp)(http) BW
GSE226718_C004-r1_4f_S3_R1.bw 179.1 Mb (ftp)(http) BW
GSE226718_C004-r1_4f_S3vsS2S_R1.bw 533.2 Mb (ftp)(http) BW
GSE226718_C004-r1_4f_S4_R1.bw 190.5 Mb (ftp)(http) BW
GSE226718_C004-r2_10Kh_S2_R1.bw 132.4 Mb (ftp)(http) BW
GSE226718_C004-r2_10Kh_S3_R1.bw 139.5 Mb (ftp)(http) BW
GSE226718_C004-r2_10Kh_S3vsS2_R1.bw 533.9 Mb (ftp)(http) BW
GSE226718_C004-r2_10Kh_S4_R1.bw 119.6 Mb (ftp)(http) BW
GSE226718_C004-r2_4f_S2L_R1.bw 173.3 Mb (ftp)(http) BW
GSE226718_C004-r2_4f_S2S_R1.bw 158.9 Mb (ftp)(http) BW
GSE226718_C004-r2_4f_S3_R1.bw 162.4 Mb (ftp)(http) BW
GSE226718_C004-r2_4f_S3vsS2S_R1.bw 533.1 Mb (ftp)(http) BW
GSE226718_C004-r2_4f_S4_R1.bw 173.2 Mb (ftp)(http) BW
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