Synthetic STARR-seq thyroid hormone response-element screen in HEK293 cells
Functional Definition of Thyroid Hormone Response Elements Based on a Synthetic STARR-seq ScreenA degenerate DR4-like response-element library (5′NGGTCANNNNRGGNNA3′; 32,768 possible combinations) was cloned into the hSTARR-seq-ORI vector and transfected into HEK293 cells. The deposited data contain input-library counts and vector-transcript output counts for 600 ng and 1,200 ng library transfections with or without 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
1e-8 M T3 (triiodothyronine) versus no T3; input library control
Episomal synthetic STARR-seq using the hSTARR-seq-ORI vector, whose cryptic minimal promoter produces a transcript containing the inserted response element in its 3′ noncoding region. A 105-nt oligonucleotide containing the degenerate DR4 motif was cloned with AgeI and SalI; HEK293 cells were co-transfected with pSG5TRα1 and pSG5RXRα expression plasmids. T3 was added 6 hours after transfection, vector-derived RNA was reverse-transcribed and amplified, and MiSeq paired-end reads were merged and counted by sequence. Deposited conditions are Lib7 input, Lib1/Lib2 600 ng no-T3/T3, and Lib3/Lib4 1,200 ng no-T3/T3.
Processed data
50 rows per page. Click a cell to inspect its full value.
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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 · 24 definitions
- element_id
- Stable package identifier assigned to each retained synthetic response-element sequence.
- sequence
- Observed 16-nt synthetic DR4-like element in 5′ to 3′ orientation; expected pattern [ACGT]GGTCA[ACGT]{4}[AG]GG[ACGT]{2}A.
- sequence_length
- Length of the synthetic element in nucleotides.
- position_1_base
- Base at variable motif position 1.
- spacer_sequence_positions_7_10
- Four-nucleotide spacer at motif positions 7–10 between the two half-sites.
- position_11_base
- Base at motif position 11, the designed R (A/G) position of the downstream half-site.
- positions_14_15_bases
- Two variable bases at motif positions 14–15 of the downstream half-site.
- input_library_count
- Observed occurrence count in the deposited Lib7 input plasmid library.
- input_library_cpm
- Input-library count normalized to counts per million using the total deposited Lib7 count.
- no_t3_600ng_count
- Observed occurrence count in GSM5861241/Lib1 output from a 600 ng library transfection without T3.
- no_t3_600ng_cpm
- GSM5861241/Lib1 output count normalized to counts per million.
- t3_600ng_count
- Observed occurrence count in GSM5861242/Lib2 output from a 600 ng library transfection with T3.
- t3_600ng_cpm
- GSM5861242/Lib2 output count normalized to counts per million.
- no_t3_1200ng_count
- Observed occurrence count in GSM5861243/Lib3 output from a 1,200 ng library transfection without T3.
- no_t3_1200ng_cpm
- GSM5861243/Lib3 output count normalized to counts per million.
- t3_1200ng_count
- Observed occurrence count in GSM5861244/Lib4 output from a 1,200 ng library transfection with T3.
- t3_1200ng_cpm
- GSM5861244/Lib4 output count normalized to counts per million.
- log2_activity_no_t3_600ng
- Descriptive log2 RNA/input activity for the 600 ng no-T3 condition: log2((no-T3 CPM + 0.5)/(input CPM + 0.5)).
- log2_activity_t3_600ng
- Descriptive log2 RNA/input activity for the 600 ng T3 condition: log2((T3 CPM + 0.5)/(input CPM + 0.5)).
- t3_response_log2fc_600ng
- Descriptive log2 T3 response at 600 ng: log2((T3 CPM + 0.5)/(no-T3 CPM + 0.5)).
- log2_activity_no_t3_1200ng
- Descriptive log2 RNA/input activity for the 1,200 ng no-T3 condition: log2((no-T3 CPM + 0.5)/(input CPM + 0.5)).
- log2_activity_t3_1200ng
- Descriptive log2 RNA/input activity for the 1,200 ng T3 condition: log2((T3 CPM + 0.5)/(input CPM + 0.5)).
- t3_response_log2fc_1200ng
- Descriptive log2 T3 response at 1,200 ng: log2((T3 CPM + 0.5)/(no-T3 CPM + 0.5)).
- qc_pass
- TRUE for a row retained after the motif-pattern and input-presence QC filter.
Quality control
The authors report paired-end read merging, curation for 20/20 identity at conserved positions around the DR4 element, occurrence counting, and DESeq2 analysis of differential representation. For this package, only input-library sequences with count >0 matching the designed 16-nt pattern [ACGT]GGTCA[ACGT]{4}[AG]GG[ACGT]{2}A were retained: 9,094 rows from 9,129 input rows (35 input rows excluded). Output-only sequences and sequences failing the motif-pattern check were excluded from table.csv; zero output counts for retained input elements were preserved as non-detections. CPM values use the full deposited sample totals (input 253,041; 600 ng no-T3 195,254; 600 ng T3 311,957; 1,200 ng no-T3 266,215; 1,200 ng T3 297,817). Derived log2 activity and T3-response values use a 0.5 CPM pseudocount and are descriptive scores, not fitted DESeq2 statistics.
Curation notes
The paper describes six cDNA output libraries from duplicate 0.6, 1.2, and 2.4 µg transfections with and without T3, but the public GEO series deposits only four output count tables (0.6 and 1.2 µg ±T3) plus the input library; no 2.4 µg table was found. The GEO input count total is 253,041, whereas the article reports 1,078,919 input reads, so this package preserves and analyzes the deposited count table without attempting to reconstruct missing reads or impute replicates. The library is synthetic; its constant flanking sequence was copied from a mouse Hairless DR4 locus, but individual tested elements have no genomic coordinates. HEK293 was resolved to Cellosaurus CVCL:0045. The paper-cited Figshare DOI is retained in the study links and manifest, while the GEO tables provide the directly downloadable MPRA/STARR-seq counts used here.