SATB1-regulated transcriptome datasets of Rcho-1 rat trophoblast stem cells

• Published in: Data in brief 2019-12, Vol.27, p.104749-104749, Article 104749
• Main Authors: Ghosh, Subhra, Chakravarthi, V. Praveen, Rai, Shubham, Roy, Richita, Pathak, Shyam, Ratri, Anamika, Rumi, M.A. Karim
• Format: Article
• Language: English
• Subjects: Biochemistry, Genetics and Molecular Biology; RNA-sequencing; SATB homeobox 1; shRNAs; Transcriptome analysis; Trophoblast stem cells
• ISSN: 2352-3409; 2352-3409
• DOI: 10.1016/j.dib.2019.104749

SATB homeobox 1 (SATB1) and its heterodimeric partner SATB2 play an important regulatory role in maintaining proliferation of trophoblast stem (TS) cells and in inhibiting trophoblast differentiation. To identify the SATB-regulated genes in TS cells, we studied the transcriptome changes in a ‘loss of function’ model of Rcho-1 rat TS cell line. Satb1 gene expression was silenced by lentiviral delivery of shRNAs targeted to exon 9 and exon 12. An Egfp shRNA was used as a non-targeted control. Total RNA was purified from shRNA-transduced Rcho-1 cells, and whole transcriptome was assessed by RNA-sequencing on an Illumina HiSeq X platform. Differentially expressed genes in Satb1 shRNA-transduced cells were identified by analyses of the RNA-sequencing data using CLC Genomics Workbench. Differentially expressed genes with each of the two different shRNAs were compared to identify SATB1-target genes and to eliminate the potential off-targets of the shRNAs. These datasets can be used to identify the SATB-regulated genes in TS cells and to understand the molecular mechanisms that regulate trophoblast proliferation and inhibit differentiation.