Experiment / E0UTHBXO3Standard STARR-seq

U2OS allele-focused osteoporosis SNP STARR-seq screen

Integrative high-throughput enhancer surveying and functional verification divulges a YY2-condensed regulatory axis conferring risk for osteoporosis

An episomal STARR-seq library tested 150-bp oligonucleotides centered on reference and alternative alleles of 5,642 prioritized osteoporosis-associated SNPs in the human osteosarcoma-derived U2OS cell line. The experiment measured plasmid input and transcribed output in three biological replicates each; the packaged table contains the 319 published allele-biased enhancer SNPs joined to their oligos, allele-level activity results, and public GEO UMI counts.

Download processed table (CSV)Raw source data API documentation

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.

Organism: Human
Taxonomy ID: NCBITaxon:9606
Biosample: CVCL:0042
Reference genome: hg19
Design focus: Variant-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated

Adapted hSTARR-seq_ORI episomal self-transcribing reporter with a 120-bp genomic sequence centered on each SNP and 15-bp adapters on both sides, yielding 150-bp oligonucleotides. The library contained 11,284 reference/alternative oligos for 5,642 SNPs. U2OS cells were transfected with 12 micrograms of library DNA into 3.6 x 10^6 cells; input plasmid DNA was sampled before transfection and poly(A) RNA output was sampled 24 h later. Three biological replicates were prepared for each input/output class and sequenced as Illumina NovaSeq 6000 PE150 libraries. Random 13-bp UMIs were used to deduplicate PCR products, and an 8-bp sample barcode separated replicates.

Processed data

50 rows per page. Click a cell to inspect its full value.

Search table valuesFilter columnOperatorValue

Visible columns (64 of 64)

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

Page 1 · 50 rows · More results available

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

Column dictionary · 64 definitions

snp_id: dbSNP identifier for the published baaSNP.
cytoband: Cytogenetic band reported in Table S8.
allele_a: First allele in the Table S8 allele_A/allele_B comparison.
allele_b: Second allele in the Table S8 allele_A/allele_B comparison.
allelic_comparison: Human-readable allele A versus allele B comparison.
allelic_effect_direction: Direction derived from the sign of Table S8 allelic log2FC; allele_a_higher or allele_b_higher.
allelic_log2fc_a_vs_b: Table S8 MPRAnalyze log2 fold change for allele A versus allele B; blank where the source reports NA because Pvalue/FDR equals zero.
allelic_statistic: Table S8 MPRAnalyze likelihood-ratio-test statistic.
allelic_pvalue: Table S8 MPRAnalyze P value.
allelic_fdr: Table S8 MPRAnalyze FDR-adjusted P value.
chromatin_interaction_genes: Genes linked to the baaSNP by promoter chromatin interactions, as reported in Table S8.
nonnearest_chromatin_interaction_genes: Table S8 subset of chromatin-interaction genes that are not the located or nearest gene; a dash is retained when reported.
insert_length_bp: Length of each synthesized oligonucleotide from Table S5, including adapters.
allele_a_sequence_5to3: 150-bp allele A oligonucleotide sequence from Table S5, written 5-prime to 3-prime.
allele_b_sequence_5to3: 150-bp allele B oligonucleotide sequence from Table S5, written 5-prime to 3-prime.
s7_allele_a_input1: Table S7 input-library activity value for allele A, biological replicate 1.
s7_allele_a_input2: Table S7 input-library activity value for allele A, biological replicate 2.
s7_allele_a_input3: Table S7 input-library activity value for allele A, biological replicate 3.
s7_allele_a_output1: Table S7 output-library activity value for allele A, biological replicate 1.
s7_allele_a_output2: Table S7 output-library activity value for allele A, biological replicate 2.
s7_allele_a_output3: Table S7 output-library activity value for allele A, biological replicate 3.
s7_allele_a_log2fc: Table S7 voom log2 fold change for output versus input for allele A.
s7_allele_a_aveexpr: Table S7 average expression value for allele A.
s7_allele_a_t: Table S7 moderated t-statistic for allele A output versus input.
s7_allele_a_pvalue: Table S7 P value for allele A output versus input.
s7_allele_a_fdr: Table S7 FDR-adjusted P value for allele A output versus input.
s7_allele_a_typea: Table S7 activity class for allele A: enhancer, silencer, or inactive.
geo_allele_a_input1_umi: GEO processed unique-UMI count for allele A in input replicate 1.
geo_allele_a_input2_umi: GEO processed unique-UMI count for allele A in input replicate 2.
geo_allele_a_input3_umi: GEO processed unique-UMI count for allele A in input replicate 3.
geo_allele_a_output1_umi: GEO processed unique-UMI count for allele A in output replicate 1.
geo_allele_a_output2_umi: GEO processed unique-UMI count for allele A in output replicate 2.
geo_allele_a_output3_umi: GEO processed unique-UMI count for allele A in output replicate 3.
geo_allele_a_input_total_umi: Sum of the three GEO input UMI counts for allele A.
geo_allele_a_output_total_umi: Sum of the three GEO output UMI counts for allele A.
geo_allele_a_total_umi: Sum of all six GEO input/output UMI counts for allele A.
s7_allele_b_input1: Table S7 input-library activity value for allele B, biological replicate 1.
s7_allele_b_input2: Table S7 input-library activity value for allele B, biological replicate 2.
s7_allele_b_input3: Table S7 input-library activity value for allele B, biological replicate 3.
s7_allele_b_output1: Table S7 output-library activity value for allele B, biological replicate 1.
s7_allele_b_output2: Table S7 output-library activity value for allele B, biological replicate 2.
s7_allele_b_output3: Table S7 output-library activity value for allele B, biological replicate 3.
s7_allele_b_log2fc: Table S7 voom log2 fold change for output versus input for allele B.
s7_allele_b_aveexpr: Table S7 average expression value for allele B.
s7_allele_b_t: Table S7 moderated t-statistic for allele B.
s7_allele_b_pvalue: Table S7 P value for allele B output versus input.
s7_allele_b_fdr: Table S7 FDR-adjusted P value for allele B output versus input.
s7_allele_b_typea: Table S7 activity class for allele B: enhancer, silencer, or inactive.
geo_allele_b_input1_umi: GEO processed unique-UMI count for allele B in input replicate 1.
geo_allele_b_input2_umi: GEO processed unique-UMI count for allele B in input replicate 2.
geo_allele_b_input3_umi: GEO processed unique-UMI count for allele B in input replicate 3.
geo_allele_b_output1_umi: GEO processed unique-UMI count for allele B in output replicate 1.
geo_allele_b_output2_umi: GEO processed unique-UMI count for allele B in output replicate 2.
geo_allele_b_output3_umi: GEO processed unique-UMI count for allele B in output replicate 3.
geo_allele_b_input_total_umi: Sum of the three GEO input UMI counts for allele B.
geo_allele_b_output_total_umi: Sum of the three GEO output UMI counts for allele B.
geo_allele_b_total_umi: Sum of all six GEO input/output UMI counts for allele B.
allele_a_s7_present: Whether the allele A row is present in published Table S7.
allele_b_s7_present: Whether the allele B row is present in published Table S7.
allele_a_geo_count_present: Whether the allele A row is present in the public GEO processed UMI table.
allele_b_geo_count_present: Whether the allele B row is present in the public GEO processed UMI table.
qc_pass: Package QC flag; true for every retained Table S8 baaSNP row.
allelic_log2fc_status: Whether the Table S8 allelic log2FC was reported or was unavailable because the source P value/FDR was zero.
source_tables: Source datasets joined to create the row: Table S8, Table S7, Table S5, and GEO processed UMI counts.

Quality control

The source pipeline separated reads by 8-bp sample barcode with no more than two mismatches/deletions (96.93%-98.82% exact barcode matching), filtered low-quality reads with fastp Q30 settings (-q 30 -u 50), extracted 120-bp SNP fragments, used the 13-bp UMI to remove PCR duplicates, and retained only reads matching the selected SNP library at 100% with Bowtie2. Alleles with no expression in any sample or pooled input/output expression below 10 were excluded by the study. Table S7 defined an enhancer as output-versus-input log2FC > 0.585 at FDR < 0.05 and a silencer as log2FC < -0.585 at FDR < 0.05; Table S8 called allele-biased enhancer SNPs with MPRAnalyze likelihood-ratio-test FDR < 0.05. For this package, rows were retained only when the Table S8 SNP ID and two-base allele pair were valid, Table S8 statistic/Pvalue/FDR were numeric with FDR < 0.05, and both Table S5 150-bp oligos were available. All 319 Table S8 rows passed these filters. Missing allele-level S7/GEO observations were left blank rather than imputed.

Curation notes

This study contributes one MPRA/STARR-seq experiment: a single U2OS library assay with three input and three output biological replicates. The table is intentionally one row per published Table S8 baaSNP (319 rows), rather than a GWAS table or the full 8,420-row public expressed-allele table. All 319 source rows pass the paper's MPRAnalyze FDR < 0.05 criterion and the package's identifier, allele-pair, statistic, and 150-bp sequence checks. Table S8 reports 29 extreme effects as NA when Pvalue/FDR equals zero; these are preserved as blank allelic_log2fc_a_vs_b values with an explanatory status. The public S7/GEO expressed table contains 8420 allele rows, so 42 of the 638 allele slots for the 319 baaSNPs are unavailable there; those fields are blank and not imputed. U2OS is mapped to Cellosaurus CVCL:0042. The assay targets scattered osteoporosis-associated variants across the genome, so region_of_interest is null; hg19 is retained as the study's UCSC reference context.

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

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

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