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Series GSE135882 Query DataSets for GSE135882
Status Public on May 25, 2020
Title GPSeq Reveals the radial organization of chromatin in the cell nucleus
Organism Homo sapiens
Experiment type Other
Summary In eukaryotes, a significant portion of the genome consists of lamina-associated domains, which are preferentially located at the periphery of the cell nucleus. However, how exactly the remaining parts of the genome are radially organized in the nucleus remains largely unknown. Here, we describe a method named Genomic loci Positioning by Sequencing (GPSeq), which allows genome-wide measurements of the distance of genomic loci to the nuclear periphery. Using GPSeq, we generated reproducible maps of radial genome organization in human cells, at various resolutions, which revealed radial gradients of genetic and epigenetic features, gene expression, as well as A/B compartments and chromatin loops. We assessed the contribution of various features in predicting radiality, and found GC content to have the strongest predictive power. Finally, we show that by combining Hi-C with GPSeq information to radially position intra- and inter-chromosomal contacts revealed by Hi-C, we are able to make 3D genome structure predictions much more accurately than it was possible thus far. We conclude that GPSeq is able to reveal fundamental aspects of genome architecture.
Overall design 4 GPseq experiments (Exp1-4) were performed in HAP1 cells. 2 experiments (Exp1-2) using HindIII enzyme and the following digestion times: 10 min, 15 min, 30 min, 1 h, 2 h. 2 experiments (Exp3-4) using MboI enzyme and the following digestion times: 1 min, 5 min, 10 min, 30 min. Additional times were performed for Exp1: 45 min and 6 h. Additionally, 2 GPSeq experiments (Exp5-6) were performed on GM06990 cells using HindIII enzyme and the following digestion times: 10 min, 15 min, 30 min, 2 h. Deposited GPSeq scores were calculated using the gpseqc (v2.3.6) pipeline, available on github: . "estimated.tsv"; raw GPSeq score (prob_g column) estimated by gpseqc pipeline. "rescaled.tsv"; rescaled GPSeq score (prob_g column) estimated by gpseqc pipeline.

All deposited structures were generated starting from Hi-C data available from the 4DN project (accession #: 4DNFI1E6NJQJ); either (* and * using only Hi-C data, or (* and * integrating Hi-C and GPSeq data coming from the first experiment (Exp1) in this series (as briefly described in the chromflock.README file). The chromflock pipeline is available on github:
Contributor(s) Girelli G, Custodio J, Kallas T, Agostini F, Wernersson E, Spanjaard B, Mota A, Kolbeinsdottir S, Gelali E, Crosetto N, Bienko M
Citation(s) 32451505
Submission date Aug 15, 2019
Last update date Jul 14, 2020
Contact name Gabriele Girelli
Organization name Karolinska Institutet / Science for Life Laboratory
Department MBB
Lab Bienko lab
Street address Tomtebodavägen 23A
City Solna
State/province Stockholm
ZIP/Postal code 17165
Country Sweden
Platforms (1)
GPL21697 NextSeq 550 (Homo sapiens)
Samples (28)
GSM4037078 Exp1_10min
GSM4037079 Exp1_15min
GSM4037080 Exp1_30min
BioProject PRJNA560398
SRA SRP218461

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SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource 97.0 Kb (ftp)(http) ZIP 8.6 Mb (ftp)(http) ZIP 103.8 Kb (ftp)(http) ZIP 9.1 Mb (ftp)(http) ZIP 11.8 Kb (ftp)(http) ZIP 96.2 Kb (ftp)(http) ZIP 8.5 Mb (ftp)(http) ZIP 103.2 Kb (ftp)(http) ZIP 9.0 Mb (ftp)(http) ZIP 11.8 Kb (ftp)(http) ZIP 92.6 Kb (ftp)(http) ZIP 8.2 Mb (ftp)(http) ZIP 96.7 Kb (ftp)(http) ZIP 8.5 Mb (ftp)(http) ZIP 11.0 Kb (ftp)(http) ZIP 59.4 Kb (ftp)(http) ZIP 8.4 Mb (ftp)(http) ZIP 97.3 Kb (ftp)(http) ZIP 8.6 Mb (ftp)(http) ZIP 11.1 Kb (ftp)(http) ZIP 4.1 Mb (ftp)(http) ZIP 4.1 Mb (ftp)(http) ZIP
GSE135882_RAW.tar 826.3 Mb (http)(custom) TAR (of BED) 468.8 Mb (ftp)(http) ZIP 567.3 Mb (ftp)(http) ZIP 567.5 Mb (ftp)(http) ZIP 470.1 Mb (ftp)(http) ZIP 988 b (ftp)(http) TXT
GSE135882_chromflock.metadata.csv.gz 6.4 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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