Experiment / E4LMJIEFJStandard STARR-seq

Human HCT116 oligo UMI-STARR-seq motif-mutagenesis library

DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers

A Twist-synthesized library of 249-bp human enhancer wild-type and motif-mutant sequences, together with negative genomic controls, was tested in HCT116 cells in two biological replicates. The processed table retains oligos with sufficient plasmid-input coverage and complete author-supplied log2 activity values.

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:0291
Reference genome: hg19
Design focus: Synthetic / Motif-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated

The human oligo library was cloned into a human STARR-seq plasmid with the ORI in place of the core promoter. HCT116 cells were electroporated with the library, incubated for 6 hours, and poly-A reporter RNA was measured alongside plasmid DNA input. Paired-end 150-bp reads were mapped to exact wild-type/mutant oligo sequences and collapsed by 10-bp UMIs; DESeq2 activity used two biological replicates and negative-region counts as inter-sample scaling factors.

Processed data

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

Visible columns (14 of 14)

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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 · 14 definitions

oligo_id: Unique identifier for the synthesized human oligo construct.
sequence_id: Parent hg19 enhancer or genomic-region identifier shared by related wild-type and mutant oligos.
strand: Orientation of the oligo relative to the reference sequence.
library_experiment: Library design category, such as all-instance mutation, individual-instance mutation, negative region, or wild-type enhancer.
sequence: 249-bp human enhancer or control sequence inserted into the STARR-seq reporter.
motif_mutated: Motif or control sequence targeted by the mutation; '-' denotes no motif annotation in the source row.
number_of_instances: Number of motif instances targeted in the construct, as supplied by GEO.
mutant_version: Identifier for the shuffled motif version used in a mutant construct.
input_rep1_umi: Replicate 1 plasmid DNA input UMI count.
input_rep2_umi: Replicate 2 plasmid DNA input UMI count.
starrseq_rep1_umi: Replicate 1 reporter-RNA UMI count.
starrseq_rep2_umi: Replicate 2 reporter-RNA UMI count.
log2_activity: DESeq2 log2 reporter-RNA versus plasmid-input activity for the HCT116 screen.
qc_pass: TRUE for oligos with at least 10 UMI reads in both input replicates and a nonmissing activity value.

Quality control

The authors retained oligo mappings with correct length and strand and no mismatches after UMI collapsing, required at least 10 UMI reads in both input replicates, added a one-read pseudocount to zero RNA counts, and calculated log2 reporter activity over input with DESeq2 and negative-region scaling. The final author workflow removed oligos without an activity result; the processed table retains 21,533 of 22,900 GEO oligos and excludes the remaining low-input or incomplete rows.

Curation notes

HCT116 is mapped to the parental HCT 116 Cellosaurus entry CVCL:0291. The GEO matrix contains 22,900 rows across four library categories; 21,533 pass the author input-coverage/activity QC and are included. The human library is selected across scattered hg19 enhancer loci, so no single continuous region is assigned.

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