Targeted SNP-STARR-seq in human SW620 cells used 120-bp genomic fragments centered on candidate noncoding SNPs, with synthesized reference and alternative alleles cloned into the hORI-STARR-seq reporter. Allele-specific enhancer activity was quantified from normalized RNA/DNA EAS 36 hours after transfection.
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:0547
Reference genome
hg19
Design focus
Variant-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Basal / Untreated; reference versus alternative allele reporter oligos
The 120-bp synthetic genomic fragments were cloned into the hORI-STARR-seq plasmid. Three biological replicates and three technical PCR replicates were performed per cell line; enhancer activity score (EAS) was calculated from DESeq2-normalized RNA and DNA counts as (RNA + 1)/DNA.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (10 of 10)
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 · 10 definitions
variant_id
dbSNP rs identifier for the tested SNP.
reference_allele
Reference nucleotide allele.
alternative_allele
Alternative nucleotide allele.
log2_alt_ref
Source-reported log2 ratio of alternative-allele versus reference-allele enhancer activity score.
p_value
Raw two-sided t-test P value for allele-specific enhancer activity.
p_adjusted
Multiple-testing-adjusted P value from the source table.
reference_enhancer_score
Enhancer activity score for the reference allele, based on normalized RNA/DNA counts.
alternative_enhancer_score
Enhancer activity score for the alternative allele, based on normalized RNA/DNA counts.
cell_line
Cell line represented by this experiment.
source_table
Supplementary workbook and worksheet of origin.
Quality control
The authors aligned reads to a custom oligonucleotide library with Bowtie2 2.5.2, normalized input DNA and output RNA counts with DESeq2 1.40.0, assessed replicate reproducibility by hierarchical clustering, and selected allele-differential results using two-sided t tests with adjusted P < 0.05. Packaging QC retained 3759/3759 rows from the Table S3 SW620 worksheet after requiring a valid rsID, distinct A/C/G/T alleles, finite effect and enhancer-score values, finite probabilities in [0,1], and p_adjusted < 0.05; no rows were removed.
Curation notes
Table S3 is a significant-result table rather than the complete 30,790-SNP count matrix; this worksheet contains the reported SW620 hits. SW620 is the metastatic cell line derived from the same patient as SW480, making this a metastasis-context experiment.