SOSHI-seq Library 1: TRα1/TRβ1 response to T3
SOSHI-seq: a high-throughput screening assay to test the functionality of putative response elements for nuclear hormone receptorsA 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.
Processed tables are specific to each experiment. Column names, units, measurements, and table structure are not standardized across the database. Check this experiment’s column definitions and quality-control notes before comparing or combining data.
Perturbation & assay details
10 nM T3 (3,3′,5-triiodo-L-thyronine) for approximately 24 h versus no T3
SOSHI-seq is a hormone-response adaptation of STARR-seq. Chemically synthesized 200-mer oligos contained approximately 158 nt of mouse genomic sequence plus common amplification flanks and were cloned into the transcribed portion of pSTARRseq-ori (Addgene #71509). HEK293 cells were co-transfected with the library, human RXRα, and either TRα1 or TRβ1 expression plasmid; T3 was added 6 h after transfection. Reporter RNA was reverse-transcribed, amplified, sequenced as single-end MiSeq reads, and counted after unique mapping to mouse GRCm38/mm10.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (50 of 50)
| Row | ||||||||||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 4 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 5 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 6 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 7 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 8 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 9 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 10 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 11 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 12 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 13 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 14 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 15 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 16 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 17 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 18 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 19 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 20 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 21 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 22 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 23 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 24 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 25 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 26 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 27 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 28 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 29 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 30 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 31 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 32 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 33 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 34 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 35 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 36 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 37 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 38 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 39 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 40 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 41 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 42 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 43 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 44 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 45 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 46 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 47 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 48 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 49 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| 50 |
Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.
Column dictionary · 50 definitions
- fragment_number
- Original numeric fragment number from the Library 1 description table.
- element_id
- Unique tested genomic fragment identifier (Lib1-n).
- chromosome
- Mouse chromosome of the tested fragment.
- start
- Start coordinate of the tested fragment on GRCm38/mm10.
- end
- End coordinate of the tested fragment on GRCm38/mm10.
- sequence
- Tested mouse genomic insert sequence.
- sequence_length_bp
- Length of the tested insert in base pairs.
- closest_gene
- Closest annotated gene supplied by the study.
- distance_to_tss_bp
- Signed distance from the fragment to the closest gene transcription start site in base pairs.
- second_closest_gene
- Second closest annotated gene supplied by the study.
- distance_to_second_tss_bp
- Signed distance from the fragment to the second closest gene transcription start site in base pairs.
- dr4_orientation
- Orientation of the study-supplied FIMO DR4 hit (+ or −).
- dr4_start_in_fragment
- 1-based start of the study-supplied DR4 hit within the insert.
- dr4_end_in_fragment
- 1-based end of the study-supplied DR4 hit within the insert.
- dr4_fimo_p_value
- FIMO p-value for the study-supplied DR4 hit.
- input_library_rpm
- Study-supplied reads per million for the fragment in the input library.
- qc_min_count_all_files
- Minimum raw reporter-RNA count across all eight files used for the Library 1 QC filter; all rows are at least 10.
- run25_tralpha_no_t3_count
- Raw reporter-RNA count for RUN25, TRα1/RXRα, no T3.
- run25_tralpha_t3_count
- Raw reporter-RNA count for RUN25, TRα1/RXRα, with T3.
- run25_tralpha_no_t3_rpm
- Reporter-RNA count normalized to reads per million for RUN25, TRα1/RXRα, no T3.
- run25_tralpha_t3_rpm
- Reporter-RNA count normalized to reads per million for RUN25, TRα1/RXRα, with T3.
- run25_tralpha_fold_change
- RUN25 T3/no-T3 fold change for TRα1/RXRα based on RPM.
- run25_tralpha_log2_fold_change
- Log2 of the RUN25 TRα1/RXRα RPM fold change.
- run25_trbeta_no_t3_count
- Raw reporter-RNA count for RUN25, TRβ1/RXRα, no T3.
- run25_trbeta_t3_count
- Raw reporter-RNA count for RUN25, TRβ1/RXRα, with T3.
- run25_trbeta_no_t3_rpm
- Reporter-RNA count normalized to reads per million for RUN25, TRβ1/RXRα, no T3.
- run25_trbeta_t3_rpm
- Reporter-RNA count normalized to reads per million for RUN25, TRβ1/RXRα, with T3.
- run25_trbeta_fold_change
- RUN25 T3/no-T3 fold change for TRβ1/RXRα based on RPM.
- run25_trbeta_log2_fold_change
- Log2 of the RUN25 TRβ1/RXRα RPM fold change.
- run66_tralpha_no_t3_count
- Raw reporter-RNA count for RUN66, TRα1/RXRα, no T3.
- run66_tralpha_t3_count
- Raw reporter-RNA count for RUN66, TRα1/RXRα, with T3.
- run66_tralpha_no_t3_rpm
- Reporter-RNA count normalized to reads per million for RUN66, TRα1/RXRα, no T3.
- run66_tralpha_t3_rpm
- Reporter-RNA count normalized to reads per million for RUN66, TRα1/RXRα, with T3.
- run66_tralpha_fold_change
- RUN66 T3/no-T3 fold change for TRα1/RXRα based on RPM.
- run66_tralpha_log2_fold_change
- Log2 of the RUN66 TRα1/RXRα RPM fold change.
- run66_trbeta_no_t3_count
- Raw reporter-RNA count for RUN66, TRβ1/RXRα, no T3.
- run66_trbeta_t3_count
- Raw reporter-RNA count for RUN66, TRβ1/RXRα, with T3.
- run66_trbeta_no_t3_rpm
- Reporter-RNA count normalized to reads per million for RUN66, TRβ1/RXRα, no T3.
- run66_trbeta_t3_rpm
- Reporter-RNA count normalized to reads per million for RUN66, TRβ1/RXRα, with T3.
- run66_trbeta_fold_change
- RUN66 T3/no-T3 fold change for TRβ1/RXRα based on RPM.
- run66_trbeta_log2_fold_change
- Log2 of the RUN66 TRβ1/RXRα RPM fold change.
- mean_log2_fold_change_tralpha
- Arithmetic mean of the RUN25 and RUN66 TRα1/RXRα log2 fold changes.
- mean_log2_fold_change_trbeta
- Arithmetic mean of the RUN25 and RUN66 TRβ1/RXRα log2 fold changes.
- deseq2_base_mean
- DESeq2 mean normalized abundance from the study-supplied analysis table.
- deseq2_log2_fold_change
- Study-supplied DESeq2 log2 fold-change estimate for the T3 response.
- deseq2_standard_deviation
- Study-supplied standard deviation for the DESeq2 estimate.
- deseq2_wald_statistic
- Study-supplied DESeq2 Wald statistic.
- deseq2_p_value
- Study-supplied DESeq2 p-value.
- deseq2_adjusted_p_value
- Study-supplied multiple-testing-adjusted DESeq2 p-value.
- deseq2_regulation
- Study-supplied response direction (Up, Down, or blank).
Quality control
The paper retained fragments with at least 10 reads in every one of the eight reporter-RNA count files (two batches × TRα1/TRβ1 ± T3), yielding 800 of 991 deposited Library 1 fragments. Reads that did not map uniquely were binned (<20% non-unique reads). The paper used DESeq2 with T3 treatment and batch as factors and reported source adjusted-p-value/regulation fields; only the read-depth-passing fragments are present in table.csv.
Curation notes
The HEK293 biosample is human (CVCL:0045), whereas every tested insert and genomic coordinate is mouse. RUN25 corresponds to the GEO repeat-1 samples and RUN66 to repeat-2; the source workbook labels these result blocks Exp.2 and Exp.1, respectively, so this table uses the GEO run names. The article describes this as a relative hormone-response ranking rather than an absolute enhancer activity measurement. The workbook contains a side-by-side FIMO table; only its fragment-keyed orientation/position/p-value fields were joined, while the unkeyed auxiliary field was not carried into the processed table.