A673 adapted STARR-seq allele activity screen
High-throughput functional dissection of noncoding SNPs with biased allelic enhancer activity for insulin resistance-relevant phenotypesAn episomal hSTARR-seq_ORI library containing both alleles of selected noncoding IR-associated SNPs was transfected into human A-673 cells for 24 h. Three biological replicates were sequenced as plasmid input and poly(A)+ RNA output libraries.
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
Basal / Untreated
Targeted variant library in the episomal hSTARR-seq_ORI self-transcribing reporter (Addgene plasmid 99296). Each tested SNP allele was represented by a 150-bp oligonucleotide containing a 120-bp genomic sequence centered on the SNP plus common adapters; 13-bp UMIs were added during input DNA processing or output RNA reverse transcription. The packaged table joins GEO UMI counts to the paper's voom per-allele activity calls (Table S5) and mpralm allele-contrast results (Table S6).
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (32 of 32)
| 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 · 32 definitions
- snp_id
- dbSNP identifier for the tested variant
- allele_1
- First allele in the paper's Table S6 A1 ordering; not relabeled as reference or alternate
- allele_2
- Second allele in the paper's Table S6 A2 ordering; not relabeled as reference or alternate
- region
- Cytogenetic region reported in Table S6
- allele_1_input_rep1
- Raw UMI count for allele 1 in input replicate 1
- allele_1_input_rep2
- Raw UMI count for allele 1 in input replicate 2
- allele_1_input_rep3
- Raw UMI count for allele 1 in input replicate 3
- allele_1_output_rep1
- Raw UMI count for allele 1 in output RNA replicate 1
- allele_1_output_rep2
- Raw UMI count for allele 1 in output RNA replicate 2
- allele_1_output_rep3
- Raw UMI count for allele 1 in output RNA replicate 3
- allele_1_input_mean
- Mean raw UMI count for allele 1 across the three input replicates
- allele_1_output_mean
- Mean raw UMI count for allele 1 across the three output replicates
- allele_2_input_rep1
- Raw UMI count for allele 2 in input replicate 1
- allele_2_input_rep2
- Raw UMI count for allele 2 in input replicate 2
- allele_2_input_rep3
- Raw UMI count for allele 2 in input replicate 3
- allele_2_output_rep1
- Raw UMI count for allele 2 in output RNA replicate 1
- allele_2_output_rep2
- Raw UMI count for allele 2 in output RNA replicate 2
- allele_2_output_rep3
- Raw UMI count for allele 2 in output RNA replicate 3
- allele_2_input_mean
- Mean raw UMI count for allele 2 across the three input replicates
- allele_2_output_mean
- Mean raw UMI count for allele 2 across the three output replicates
- allele_1_activity_log2fc
- Paper Table S5 log2 output/input activity effect for allele 1
- allele_1_activity_fdr
- Paper Table S5 FDR for the output-versus-input activity test for allele 1
- allele_1_activity_type
- Paper Table S5 per-allele call: eSNP, silencer, or inactive
- allele_2_activity_log2fc
- Paper Table S5 log2 output/input activity effect for allele 2
- allele_2_activity_fdr
- Paper Table S5 FDR for the output-versus-input activity test for allele 2
- allele_2_activity_type
- Paper Table S5 per-allele call: eSNP, silencer, or inactive
- allelic_log2fc_a1_vs_a2
- Paper Table S6 mpralm log2 allele effect, explicitly A1/A2; positive values favor allele 1
- allelic_aveexpr
- Paper Table S6 average expression statistic for the allele contrast
- allelic_p_value
- Paper Table S6 P value for the allele contrast
- allelic_fdr
- Paper Table S6 FDR-adjusted P value for the allele contrast
- baaSNP
- Paper Table S6 biased allelic enhancer activity call: YES or NO
- min_count_all_samples
- Minimum of the 12 raw UMI counts for both alleles across all input and output replicates; retained rows are at least 5
Quality control
The study demultiplexed paired reads by 8-bp replicate barcodes allowing up to two mismatches/deletions, filtered low-quality reads with fastp Q30 settings, extracted 13-bp UMIs and removed PCR duplicates, and retained only 100%-matched SNP sequences after Bowtie2 alignment. The paper excluded SNP alleles with fewer than 5 counts in any sample and reported replicate activity correlations of Pearson R² 0.91–0.97. For this package, a variant pair was retained only when both Table S6 alleles had at least 5 UMI counts in all 3 input and 3 output replicates (12 counts per pair); all 1,233 A673 pairs passed this package-level filter.
Curation notes
The GEO sample metadata identifies A673 as a human muscle proxy; current Cellosaurus annotation for A-673 is CVCL_0080 and notes that the line is misclassified as Ewing sarcoma, whereas the paper calls it a rhabdomyoma/muscle-derived line. Two A673 allele pairs (rs7115850 and rs4587594) have no corresponding allele-2 row in Table S5, so those per-allele activity fields are blank while the official Table S6 allele contrast and raw counts are retained. Samples are GSM5936688–GSM5936693 (input replicates 1–3 followed by output replicates 1–3). GEO records the build as h19; this package normalizes that label to hg19. The paper separately uses hg38 conservation scores for a downstream deltaSVM analysis.