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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

E-mail(s)

frank.rosenbauer@ukmuenster.de

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)

More...

GSM3496188	BMM_1_Sfpi1-Prom
GSM3496189	BMM_2_Sfpi1-Prom
GSM3496190	T-cell_1_Sfpi1-Prom

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BioProject

SRA

Download family	Format
SOFT formatted family file(s)	SOFT
MINiML formatted family file(s)	MINiML
Series Matrix File(s)	TXT

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 Selector
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record