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Series GSE75390 Query DataSets for GSE75390
Status Public on Feb 28, 2017
Title DNase-seq analysis of B3 pre-B cell line from STATegra Project
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The main goal of the project is to develop a new generation of bioinformatics resources for the integrative analysis of multiple types of omics data. These resources include both novel statistical methodologies as well as user-friendly software implementations. STATegra methods address many aspects of the omics data integration problem such as the design of multiomics experiments, integrative transcriptional and regulatory networks, integrative variable selection, data fusion, integration of public domain data, and integrative pathway analysis. To support method development STATegra uses a model biological system, namely the differentiation process of mouse pre-B-cells. The STATegra consortium generated data focused on a critical step in the differentiation of B lymphocytes, which are key components of the adaptive immune system. Transcription factors of the Ikaros family are central to the normal differentiation of B cell progenitors and their expression increases in response to developmental stage-specific signals to terminate the proliferation of B cell progenitors and to initiate their differentiation. In particular, a novel biological system that models the transition from the pre-BI stage to the pre-BII subsequent stage, where B cell progenitors undergo growth arrest and differentiation, was used. The approach involves a pre-B cell line, B3 , and an inducible version of the Ikaros transcription factor, Ikaros-ERt2. Ikaros factors act to down-regulate genes that drive proliferation and to simultaneously up-regulate the expression of genes that promote the differentiation of B cell progenitors. Hence, in the B3 system, before induction of Ikaros, cells proliferate and their gene expression pattern is similar to proliferating B cell progenitors in vivo. Following Ikaros induction, B3 cells undergo gene expression changes that resemble those that occur in vivo during the transition from cycling to resting pre-B cells, followed by a marked reduction in cellular proliferation and by G1 arrest. On this system the consortium has created a high-quality data collection consisting of a replicated time course using seven different omics platforms: RNA-seq, miRNA-seq, ChIP-seq, DNase-seq, Methyl-seq, proteomics and metabolomics, which is used to assess and to validate STATegra methods.
Overall design The STATegra experimental design consists of a 6 points time course that captures the differentiation of B3 cells containing Ikaros-ERt2 upon Ikaros induction within a 24 hours period. The process was sampled at 0h, 2h, 6h, 12h, 18h and 24h after Ikaros induction by Tamoxifen. As control, B3 cells transfected with an empty vector were treated and sampled in the same way as the inducible line. Eight different omic technologies were measured on this system: RNA-seq, miRNA-seq, DNase-seq, RRBS-seq, ChIP-seq, scRNA-seq, Proteomics and Metabolomics. Generally, three biological replicates were obtained per platform and were processed as independent batches.
For each DNAse-seq sample, 3 biological replicates (R4, R5 and R6) were generated and sequenced as paired-end on the NextSeq 500 Illumina platform. Additionally, some Ikaros samples (corresponding to R4) were re-sequenced in order to improve the coverage.
Web link
Contributor(s) Mortazavi A, Ramírez R, Zeng W, El-Ali N, Tegnér J, Gómez-Cabrero D, Silderberg G, Tarazona S, Conesa A
Citation(s) 31672995
Submission date Nov 25, 2015
Last update date Oct 05, 2020
Contact name Ana Conesa
Organization name Centro de Investigaciones Príncipe Felipe (CIPF)
Department Computational Genomics Program
Lab Genomics and Gene Expression Lab
Street address C/ Eduardo Primo Yúfera 3
City Valencia
State/province Valencia
ZIP/Postal code 46012
Country Spain
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (36)
GSM1954299 STATegra Control cells 0h Batch11
GSM1954300 STATegra Control cells 0h Batch12
GSM1954301 STATegra Control cells 0h Batch13
This SubSeries is part of SuperSeries:
GSE75395 Omics analyses of B3 pre-B cell line from STATegra Project
BioProject PRJNA304100
SRA SRP066657

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE75390_STAT_DNaseSeq_homer_RPKM_TMM_ARSyN.txt.gz 14.7 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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