A synthetic library of 120-bp sequences centered on 2,034 prioritized central-obesity SNPs, with both alleles represented, was tested in human preadipocytes derived from subcutaneous adipose tissue. Plasmid input DNA and 24-hour poly(A) RNA output were measured by UMI-tagged STARR-seq in three biological replicates; the processed table retains the 2,534 allele fragments represented in the paper's QC-passing activity table.
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
CL:0002583
Reference genome
hg19
Design focus
Variant-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Basal / Untreated
Episomal hSTARR-seq_ORI plasmid assay using 150-bp synthesized oligos: a 120-bp SNP-centered human genomic fragment flanked by identical 15-bp adapters. Reference and alternative allele constructs were transfected into 1.0 × 10^7 human subcutaneous preadipocytes; plasmid input was sampled before transfection and poly(A) RNA output was collected 24 h later. Reverse-transcription UMIs and 8-bp library barcodes were used for deduplication and demultiplexing. Perfectly matched 120-bp reads were counted with Bowtie 2.4.1 alignment support, and enhancer activity was modeled with limma/voom across three input and three output replicate libraries on an Illumina NovaSeq 6000.
Processed data
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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 · 36 definitions
element_id
Exact GEO count-table identifier in the form rsID|chromosome:start-end|tested allele.
rsid
dbSNP rs identifier for the tested SNP.
chromosome
Chromosome reported in the Table S7 hg19 oligo coordinate.
element_start_hg19
1-based start of the 120-bp tested fragment on hg19.
element_end_hg19
1-based end of the 120-bp tested fragment on hg19.
tested_allele
Allele represented by this row's synthesized 120-bp fragment.
paired_allele
The other allele synthesized for the same SNP and coordinate in Table S7; NA when not applicable.
paired_allele_qc_pass
Boolean indicating whether the paired allele also appears in the QC-passing Table S8 result set.
sequence_120bp
SNP-centered genomic sequence used in the reporter after removal of the two 15-bp synthesis adapters.
input_rep1_umi
Unique UMI count in plasmid input replicate 1.
input_rep2_umi
Unique UMI count in plasmid input replicate 2.
input_rep3_umi
Unique UMI count in plasmid input replicate 3.
output_rep1_umi
Unique UMI count in RNA output replicate 1.
output_rep2_umi
Unique UMI count in RNA output replicate 2.
output_rep3_umi
Unique UMI count in RNA output replicate 3.
input_pooled_umi
Sum of the three plasmid input replicate UMI counts.
output_pooled_umi
Sum of the three RNA output replicate UMI counts.
input_mean_umi
Mean plasmid input UMI count across the three replicates.
output_mean_umi
Mean RNA output UMI count across the three replicates.
pooled_log2_output_input
Unnormalized log2 ratio of pooled RNA output UMI count to pooled plasmid input UMI count.
activity_log2fc
Published Table S8 limma/voom log2 fold-change activity estimate for output relative to input.
activity_average_expression
Published Table S8 average expression value from the limma model.
activity_t
Published moderated t statistic for the Table S8 output-versus-input activity test.
activity_p_value
Published raw p-value for the Table S8 activity test.
activity_fdr
Published Benjamini-Hochberg FDR for the Table S8 activity test.
enhancer_fragment
Published Table S8 enhancer-fragment call (Yes/No; activity threshold FC >1.5 and FDR <0.05).
allele_a
Allele A in the paper's Table S9 allelic comparison; NA for SNPs without a published allelic result.
allele_b
Allele B in the paper's Table S9 allelic comparison; NA for SNPs without a published allelic result.
allelic_effect_fc_a_vs_b
Published Table S9 allelic activity fold change, defined as (output A/output B)/(input A/input B).
allelic_effect_log2fc_a_vs_b
Log2 transform of the published Table S9 allele-A-versus-allele-B fold change.
tested_allele_vs_other_log2fc
Signed Table S9 allelic log2 effect for this row's tested allele versus its paired allele; positive means the tested allele has higher activity.
allelic_effect_p_value
Published Fisher's exact-test p-value for the Table S9 allelic comparison.
allelic_effect_fdr
Published FDR for the Table S9 allelic comparison.
allelic_significant_fdr_0_05
Boolean indicating the published Table S9 allelic comparison has FDR <0.05; NA when no S9 result exists.
tested_allele_effect_direction
Direction of the tested allele relative to its paired allele for a published Table S9 contrast.
source_table
Source files and supplementary tables used to construct the row.
Quality control
The authors used 100%-matched reads for unique UMI counting, stated that alleles without expression in a replicate or with pooled input/output counts below 10 were removed, modeled activity with limma/voom, and used Benjamini-Hochberg FDR < 0.05. Enhancer fragments were called at output-versus-input fold change >1.5 and FDR <0.05; allelic activity was tested with Fisher's exact test and FDR <0.05. Package QC follows the published Table S8 result set: it retains only Table S7 library constructs with pooled Input UMI count >=10 and pooled Output UMI count >=10, yielding 2,534 of 4,068 synthesized allele constructs and exactly reproducing the 2,534 S8 rows. Individual replicate zero counts were retained when the pooled threshold passed because such rows are present in the published S8 table. Four baseline controls and 142 count-file rows that do not match the listed Table S7 library were excluded from the variant table.
Curation notes
The paper describes the cells as human preadipocytes derived from healthy-subject subcutaneous adipose tissue purchased from BLUEFBIO, not as an immortalized line; this was resolved to Cell Ontology CL:0002583 (subcutaneous preadipocyte). Table S7 does not label the two constructs as reference versus alternate, so the table deliberately uses tested_allele/paired_allele and the paper's allele A/B labels rather than inferring REF/ALT. Table S8 contains 1,301 enhancer-called allele rows representing 791 SNPs; its 2,534 rows are the source's analyzed fragment set. Table S9 contributes 141 SNP-level allelic effects, repeated on each passing allele row with a signed tested_allele_vs_other_log2fc. The GEO count file additionally contains 4 baseline controls and 1,826 variant identifiers not listed in Table S7; only the 2,534 S8/S7-matched rows are packaged as analyzable library constructs. Raw sequencing reads were not included, consistent with the ingestion request.