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Series GSE123131 Query DataSets for GSE123131
Status Public on May 29, 2019
Title Benchmarking of 4C-seq pipelines based on real and simulated data
Platform organism Mus musculus
Sample organisms Homo sapiens; Mus musculus
Experiment type Other
Third-party reanalysis
Summary With its capacity for high-resolution data output in one region of interest, chromosome conformation capture combined with high-throughput sequencing (4C-seq) is a state-of-the-art next-generation sequencing technique that provides epigenetic insights, and regularly advances current medical research. However, 4C-seq data is complex and prone to biases, and while specialized programs exist, an unbiased, extensive benchmarking is still lacking. Furthermore, neither substantial datasets with fully characterized ground truth, nor simulation programs for realistic 4C-seq data have been published. We conducted a benchmarking study on 54 4C-seq samples from 12 datasets, including original murine BMM, T-cell, and 416B data, and developed a novel 4C-seq simulation software to allow for more detailed comparisons of 4C-seq algorithms on 50 simulated datasets with 10 to 120 samples each.
Overall design 54 4C-seq samples from 12 datasets, including original murine BMM, T-cell, and 416B data. Re-analyzed samples are from GSE77265, GSE87299, SRP023622, GSE111863, GSE52595, SRA048225, GSE52457, PRJEB5236, GSE62269, GSE101423, and GSE96546. The processed data for these re-analyzed samples are available in a tar archive at the foot of this page.
Contributor(s) Walter C, Schuetzmann D, Rosenbauer F, Dugas M
Citation(s) 31134276
Submission date Nov 29, 2018
Last update date Oct 28, 2021
Contact name Frank Rosenbauer
Organization name University Hospital Münster
Department Institute of Molecular Tumor Biology
Street address Robert-Koch-Str. 43
City Münster
ZIP/Postal code 48149
Country Germany
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (6)
GSM3496188 BMM_1_Sfpi1-Prom
GSM3496189 BMM_2_Sfpi1-Prom
GSM3496190 T-cell_1_Sfpi1-Prom
Reanalysis of GSM2047012
Reanalysis of GSM2047013
Reanalysis of GSM2047014
Reanalysis of GSM2047015
Reanalysis of GSM2047016
Reanalysis of GSM2047017
Reanalysis of GSM2327522
Reanalysis of GSM2327523
Reanalysis of GSM2327524
Reanalysis of GSM2327525
Reanalysis of GSM2327526
Reanalysis of GSM2327527
Reanalysis of GSM3042017
Reanalysis of GSM3042018
Reanalysis of GSM3042019
Reanalysis of GSM3042020
Reanalysis of GSM3042021
Reanalysis of GSM3042022
Reanalysis of GSM1272326
Reanalysis of GSM1272327
Reanalysis of GSM1272324
Reanalysis of GSM1272325
Reanalysis of GSM1412881
Reanalysis of GSM1412882
Reanalysis of GSM1412885
Reanalysis of GSM1412886
Reanalysis of GSM1524258
Reanalysis of GSM1524259
Reanalysis of GSM1524256
Reanalysis of GSM1524257
Reanalysis of GSM3058518
Reanalysis of GSM3058519
Reanalysis of GSM3058520
Reanalysis of GSM3058535
Reanalysis of GSM3058536
Reanalysis of GSM3058537
Reanalysis of GSM2535354
Reanalysis of GSM2535355
Reanalysis of GSM2535350
Reanalysis of GSM2535351
BioProject PRJNA507614
SRA SRP171161

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
GSE123131_List_of_reanalyzed_samples_and_associated_processed_data.xlsx 15.6 Kb (ftp)(http) XLSX
GSE123131_RAW.tar 50.0 Kb (http)(custom) TAR (of BED)
GSE123131_re-analyzed_data.bed.tar.gz 330.0 Kb (ftp)(http) TAR
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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