Experiment / E4LBT2EFGStandard STARR-seq

SOSHI-seq Library 2: TRα1/TRβ1 response to T3

SOSHI-seq: a high-throughput screening assay to test the functionality of putative response elements for nuclear hormone receptors

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.

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Organism: Human
Taxonomy ID: NCBITaxon:9606
Biosample: CVCL:0045
Reference genome: GRCm38/mm10
Design focus: Region-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

10 nM T3 (3,3′,5-triiodo-L-thyronine) for approximately 24 h versus no T3

Library 2 used chemically synthesized 150-mer oligos containing approximately 108 nt of mouse genomic sequence plus common amplification flanks, cloned into the transcribed portion of pSTARRseq-ori (Addgene #71509). HEK293 cells were co-transfected with the library, human RXRα, and TRα1 or TRβ1 expression plasmid; T3 was added 6 h after transfection. Reporter cDNA was sequenced as single-end MiSeq reads and counted after unique mapping to mouse GRCm38/mm10. The source workbook's auxiliary FIMO block is not keyed to the tested-fragment rows and is therefore not joined into this table.

Processed data

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Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.

Column dictionary · 38 definitions

fragment_number: Original numeric fragment number from the Library 2 description table.
element_id: Unique tested genomic fragment identifier (lib2-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.
qc_min_count_all_files: Minimum raw reporter-RNA count across all six TR files used for the Library 2 QC filter; all rows are at least 10.
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.
run42_trbeta_no_t3_count: Raw reporter-RNA count for RUN42, TRβ1/RXRα, no T3.
run42_trbeta_t3_count: Raw reporter-RNA count for RUN42, TRβ1/RXRα, with T3.
run42_trbeta_no_t3_rpm: Reporter-RNA count normalized to reads per million for RUN42, TRβ1/RXRα, no T3.
run42_trbeta_t3_rpm: Reporter-RNA count normalized to reads per million for RUN42, TRβ1/RXRα, with T3.
run42_trbeta_fold_change: RUN42 T3/no-T3 fold change for TRβ1/RXRα based on RPM.
run42_trbeta_log2_fold_change: Log2 of the RUN42 TRβ1/RXRα RPM fold change.
mean_log2_fold_change_trbeta: Arithmetic mean of the RUN66 and RUN42 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 reports 936 Library 2 fragments evaluated with a minimum read count greater than 10; the deposited tables reproduce that 936-fragment count when the threshold is applied as at least 10 reads in every one of the six relevant TR reporter-RNA count files (RUN66 TRα1/TRβ1 ± T3 and RUN42 TRβ1 ± T3). Reads that did not map uniquely were binned (<20% non-unique reads). The study-supplied DESeq2 analysis used treatment and batch factors; its statistics and response labels are retained where available.

Curation notes

The HEK293 biosample is human (CVCL:0045), whereas every tested insert and genomic coordinate is mouse. RUN66 contributes the Library 2 TRα1 and TRβ1 pairs; RUN42 contributes the duplicated TRβ1 pair. Library 2's workbook has 993 actual fragments and the paper's 936-fragment coverage statement is reproduced by the all-six-file read filter. The article writes '>10' for this threshold, but five fragments have a minimum count exactly equal to 10; using >=10 reproduces the reported 936, so that operational choice is documented here. The paper's DR4/FIMO auxiliary block is not row-keyed to the Library 2 fragment table and was left in raw_data but excluded from the processed join.

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