Shijia Wu, Romain Guyot, Yanis Zekri, Wenzheng Jiang, Frédéric Flamant
We present a cheap, rapid, and versatile assay called SOSHI-seq (Screening of Self-transcribed Hormone Inducible response elements coupled to sequencing). The protocol is an adaptation of the STARR-seq method, which allows testing the capacity of thousands of synthetic DNA sequences to act as hormone-response elements. Using the nuclear receptors of thyroid hormone as an example, we show that SOSHI-seq is a suitable complement to ChIP-Seq analysis to identify at genome-wide scale the functional response elements occupied by nuclear receptors in chromatin.
Shijia Wu, Romain Guyot, Yanis Zekri, Wenzheng Jiang, Frédéric Flamant. SOSHI-seq: a high-throughput screening assay to test the functionality of putative response elements for nuclear hormone receptors. 2025-12-06. https://doi.org/10.1038/s41598-025-29970-8
The GEO series includes a Bank 2 LXRα no-ligand/T-compound reporter pair using the Library 2 oligo pool. This exploratory table reports count-normalized T-compound fold changes for the available pair; the publication and supplementary tables do not provide a DESeq2 analysis for these samples.
A second pool of approximately 1,000 shorter mouse genomic fragments selected around TR-associated DR4-containing regions was cloned into the same episomal STARR-seq reporter and tested in HEK293 cells. RUN66 measured TRα1 and TRβ1 responses, while RUN42 supplied an independent TRβ1 ± T3 batch.
A pool of approximately 1,000 mouse genomic TRα1 binding-site fragments was cloned into the transcribed region of an episomal pSTARRseq-ori reporter and tested in HEK293 cells. Two independent batches (RUN25 and RUN66) were assayed with TRα1/RXRα or TRβ1/RXRα expression, with and without 10 nM T3.
Original supplemental and deposited inputs retained for this study. Download files individually or together as a ZIP; nested folders are preserved. Source reuse terms apply, and sequencing reads may be omitted.
Download all 20 files (ZIP)GSE298259_family.txtGSE298259_series.txtGSM9010788_RUN25alphanoT3.txt.gzGSM9010789_RUN25alphawithT3.txt.gzGSM9010790_RUN25betanoT3.txt.gzGSM9010791_RUN25betawithT3.txt.gzGSM9010792_RUN42TRbetanoT3.txt.gzGSM9010793_RUN42TRbetawithT3.txt.gzGSM9010794_RUN42LXRanoLig.txt.gzGSM9010795_RUN42LXRaTcomp.txt.gzGSM9010796_RUN66alphanoT3.txt.gzGSM9010797_RUN66alphawithT3.txt.gzGSM9010798_RUN66betanoT3.txt.gzGSM9010799_RUN66betawithT3.txt.gzGSM9010800_RUN66TRalphanoT3.txt.gzGSM9010801_RUN66TRalphawithT3.txt.gzGSM9010802_RUN66TRbetanoT3.txt.gzGSM9010803_RUN66TRbetawithT3.txt.gzSupplementary_Table_S1.xlsxSupplementary_Table_S2.xlsx