U2OS-GR synthetic STARR-seq under dexamethasone and vehicle
High-throughput screening of glucocorticoid-induced enhancer activity reveals mechanisms of stress-related psychiatric disordersAn episomal synthetic STARR-seq library tested 201-bp reference and alternative alleles centered on 3,662 dexamethasone-responsive eSNP candidates, together with positive and negative control inserts, in U2OS-GR cells. This experiment compares 100 nM dexamethasone for 4 h with a 0.001% ethanol vehicle control; the packaged table contains published DRE and SNP-DRE results passing the reported statistical filters.
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
100 nM dexamethasone for 4 h versus 0.001% ethanol vehicle control
Synthetic self-transcribing reporter assay with the 201-bp genomic insert cloned downstream of a minimal promoter; active enhancer transcripts carry the tested insert sequence, so this design does not use a separate barcode. The library contained the eSNP allele constructs and positive dex-responsive, random genomic, and Markov-model random controls. U2OS-GR is a U2OS osteosarcoma derivative stably expressing glucocorticoid receptor. RNA and DNA libraries were sequenced as 150-bp paired-end reads and analyzed with MPRAnalyze 1.5.1.
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 · 31 definitions
- reported_snp_id
- SNP or coordinate-derived identifier as reported in Supplementary Tables S2 and S3.
- input_library_id
- Identifier joined to Supplementary Table S1 for the tested eSNP library element.
- assayed_cell_line
- Cell-line section from which the result was extracted.
- chromosome
- Chromosome reported in Table S1.
- position_hg19
- 1-based eSNP center coordinate on hg19 from Table S1.
- fragment_start_hg19
- Calculated inclusive start of the 201-bp insert, position_hg19 minus 100.
- fragment_end_hg19
- Calculated inclusive end of the 201-bp insert, position_hg19 plus 100.
- fragment_length_bp
- Length of the synthesized genomic insert in base pairs.
- reference_allele
- Reference allele used in the ordered insert library.
- alternative_allele
- Alternative allele used in the ordered insert library.
- dre_response_class
- Inductive, repressive, or mixed direction derived from the sign of significant Table S2 dex-versus-vehicle log2 fold changes.
- reference_dre_significant
- Whether the reference-allele insert passed the Table S2 FDR < 0.1 DRE threshold.
- reference_dex_vs_vehicle_log2fc
- Table S2 log2 fold change for dexamethasone versus vehicle for the reference-allele insert.
- reference_dex_vs_vehicle_statistic
- Table S2 comparative-test statistic for the reference-allele dex-versus-vehicle effect.
- reference_dex_vs_vehicle_pvalue
- Table S2 p-value for the reference-allele dex-versus-vehicle effect.
- reference_dex_vs_vehicle_fdr
- Table S2 FDR for the reference-allele dex-versus-vehicle effect.
- alternative_dre_significant
- Whether the alternative-allele insert passed the Table S2 FDR < 0.1 DRE threshold.
- alternative_dex_vs_vehicle_log2fc
- Table S2 log2 fold change for dexamethasone versus vehicle for the alternative-allele insert.
- alternative_dex_vs_vehicle_statistic
- Table S2 comparative-test statistic for the alternative-allele dex-versus-vehicle effect.
- alternative_dex_vs_vehicle_pvalue
- Table S2 p-value for the alternative-allele dex-versus-vehicle effect.
- alternative_dex_vs_vehicle_fdr
- Table S2 FDR for the alternative-allele dex-versus-vehicle effect.
- snp_dre_class
- Published SNP-DRE class: dex, veh, or dex/veh; blank when the element was not a passing Table S3 SNP-DRE.
- alternative_vs_reference_dex_log2fc
- Table S3 allele-dependent log2 fold change for alternative versus reference in the dexamethasone condition.
- alternative_vs_reference_dex_statistic
- Table S3 allele-dependent test statistic in the dexamethasone condition.
- alternative_vs_reference_dex_pvalue
- Table S3 allele-dependent p-value in the dexamethasone condition.
- alternative_vs_reference_dex_fdr
- Table S3 allele-dependent FDR in the dexamethasone condition.
- alternative_vs_reference_vehicle_log2fc
- Table S3 allele-dependent log2 fold change for alternative versus reference in the vehicle condition.
- alternative_vs_reference_vehicle_statistic
- Table S3 allele-dependent test statistic in the vehicle condition.
- alternative_vs_reference_vehicle_pvalue
- Table S3 allele-dependent p-value in the vehicle condition.
- alternative_vs_reference_vehicle_fdr
- Table S3 allele-dependent FDR in the vehicle condition.
- source_supplementary_tables
- Supplementary table provenance for the row: S2, or S2;S3 when allele-dependent results are available.
Quality control
The study assessed sequencing quality with FastQC, trimmed adapters with Cutadapt, stitched paired reads with FLASH 1.2.11 and retained only reads with exactly 99-bp overlap, deduplicated PCR duplicates with UMI-Tools, retained reads perfectly matching the ordered reference fragments, and filtered fragments with fewer than 10 reads. MPRAnalyze used RNA counts and the DNA plasmid library with total-sum-scaling normalization, a negative-control null model, and likelihood-ratio/comparative tests; allele-dependent effects were called at FDR < 0.1 using the Wald test. For this package, a row was retained only when at least one Table S2 allele-level FDR was < 0.1 and the locus/alleles mapped to Table S1; Table S3 fields are populated only for SNP-DREs passing the same published FDR threshold.
Curation notes
The supplementary workbook contains separate U2OS-GR and U138MG sections; this child uses only the U2OS-GR section. Table S2 contributes 508 passing DRE rows and Table S3 contributes 225 passing SNP-DRE annotations. Coordinate-derived IDs such as rs1-148283858 retain the reported ID while input_library_id preserves the matching Table S1 coordinate ID. The specific GR-transduced derivative is not separately catalogued in Cellosaurus, so the parent U2OS accession CVCL:0042 is used. The table is a published-results table rather than a raw read-count matrix and therefore does not contain all library elements or sequencing read counts; unresponsive controls and non-significant entries are omitted.