Dataset features


Application: sRNA-seq analysis
Number of samples: 36
Release date: Feb 28 2017
Last update date: Oct 10 2018
Access: Public
Genes: IKZF1, MAPK3
Taxon: Mus musculus
Dataset link miRNA-seq analysis of B3 pre-B cell line from STATegra Project

Experimental Protocol

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. Small RNA-seq analysis was performed using Trizol-extracted total RNA of 3 biological batches (4, 5 and 6) for time 0h and total RNA of 3 biological batches (1, 2 and 3) for times 2h, 6h, 12h,18h and 24h. There were two experimental conditions (C=Control, IK=Ikaros) and the 3 biological replicates per condition and time point were numbered as 1, 2 and 4. For some of these biological replicates, also technical replicates were generated in order to measure the variability between batches and afterwards correct the potential batch effect.