An episomal hSTARR-seq library comprising 12,833 190-bp fragments tiled across HCT116 essential-enhancer windows, 60 positive-control oligos for known MYC/SV40 enhancers, and 2,095 yeast ORF negative controls was electroporated into HCT116 cells in triplicate. Matched plasmid DNA and poly(A)+ reporter-RNA counts from Table S3 were used to quantify per-oligo enhancer activity.
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:0291
Reference genome
GRCh38
Design focus
Region-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Basal / Untreated
The authors cloned 190-bp oligos with constant flanking sequences into the episomal hSTARR-seq_ORI reporter (Addgene plasmid #99296), electroporated HCT116 cells with TBK1/IKK and PKR inhibitors, harvested cells 48 h later, and sequenced plasmid DNA and poly(A)+ reporter RNA. Unique molecular identifiers were incorporated during library preparation; sequencing used 2 x 100-bp paired-end reads on an Illumina NextSeq 2000, with three biological transfection replicates.
Processed data
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Column dictionary · 25 definitions
oligo_id
Oligonucleotide identifier from Table S3; genomic fragments use hg38 coordinate labels and controls use yeast ORF or SV40 labels.
element_class
Class inferred from the identifier: human_genomic_fragment, genomic_negative_control, yeast_orf_negative_control, or SV40_positive_control.
sequence_role
Role inferred from the identifier: negative_control, positive_control, or genomic_test_or_known_positive.
chromosome
Chromosome parsed from a genomic coordinate identifier; blank for synthetic yeast and SV40 controls.
start_hg38
Start coordinate parsed from the genomic oligo identifier, using the coordinate convention reported in Table S3.
end_hg38
End coordinate parsed from the genomic oligo identifier, using the coordinate convention reported in Table S3.
sequence
The 190-bp genomic or control sequence from the Table S3 oligo-sequence worksheet.
sequence_length
Length of the oligo sequence in base pairs.
plasmid_dna_count
Raw plasmid-DNA input read count from the HCT116 raw-count worksheet.
rna_rep1_count
Raw reporter-RNA read count for HCT116 biological replicate 1.
rna_rep2_count
Raw reporter-RNA read count for HCT116 biological replicate 2.
rna_rep3_count
Raw reporter-RNA read count for HCT116 biological replicate 3.
mean_rna_count
Arithmetic mean of the three raw HCT116 reporter-RNA counts.
dna_cpm
Plasmid-DNA count normalized to counts per million over the retained oligo set.
rna_rep1_cpm
Replicate-1 reporter-RNA count normalized to counts per million over the retained oligo set.
rna_rep2_cpm
Replicate-2 reporter-RNA count normalized to counts per million over the retained oligo set.
rna_rep3_cpm
Replicate-3 reporter-RNA count normalized to counts per million over the retained oligo set.
mean_rna_cpm
Arithmetic mean of the three normalized reporter-RNA CPM values.
log2_activity_rep1
Library-size-normalized log2(RNA CPM / plasmid-DNA CPM) for replicate 1.
log2_activity_rep2
Library-size-normalized log2(RNA CPM / plasmid-DNA CPM) for replicate 2.
log2_activity_rep3
Library-size-normalized log2(RNA CPM / plasmid-DNA CPM) for replicate 3.
mean_log2_activity
Mean of the three replicate log2 RNA/DNA activity values; larger values indicate greater reporter activity.
activity_sd
Population standard deviation of the three replicate log2 activity values.
activity_rank
Descending rank among retained oligos by mean_log2_activity, with 1 as the highest activity.
source_table
The Table S3 worksheets used to assemble the row: oligo sequence and raw counts HCT116.
Quality control
The paper aligned STARR-seq reads to the oligo library, removed oligos with plasmid-DNA counts <25 or RNA counts <5 in at least three biological replicate libraries, estimated dispersion from yeast ORF controls, and used edgeR negative-binomial regression with Benjamini-Hochberg adjustment and a 5% empirical FDR threshold calibrated to enriched yeast controls. The paper reports Pearson correlation >0.9 for RNA/DNA ratios across the three biological replicates. Package QC retained the 14,852 unique oligos in the Table S3 raw-count worksheet: all had finite nonnegative counts, plasmid DNA >=25 (minimum 32), and all three RNA replicate counts >=5 (minimum 6). The 14,988-row sequence worksheet was joined by oligo ID; sequence rows without a corresponding count record were excluded. The generated activity columns are descriptive library-size-normalized CPM and log2(RNA CPM/DNA CPM) values; author edgeR p-values and calls were not recreated because they are not supplied in Table S3.
Curation notes
The Cellosaurus accession for the parental HCT116 line is CVCL_0291 (represented here in the requested CURIE form CVCL:0291). The source workbook supplies raw counts only for HCT116; the paper reports a matched K562 STARR-seq comparison in Figure 4H but does not provide a K562 count worksheet or separate downloadable result table. K562 values were therefore not inferred. The human_genomic_fragment class includes candidate enhancer tiles and unlabeled known-MYC positive-control tiles because Table S3 does not distinguish those subsets in its identifiers.