Experiment / E08AKP87KStandard STARR-seq

Drosophila S2 oligo UMI-STARR-seq motif-mutagenesis and synthetic enhancer library

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

A Twist-synthesized 249-bp oligo library containing wild-type Drosophila enhancers, motif mutants, flank-swap and scanning-mutagenesis constructs, Med14 shuffle-bin constructs, and de novo synthetic enhancers was tested in S2 cells with developmental and housekeeping core promoters. Three biological replicates were performed for each promoter screen.

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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: Fruit fly
Taxonomy ID: NCBITaxon:7227
Biosample: CVCL:Z232
Reference genome: dm3
Design focus: Synthetic / Motif-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated

Episomal Drosophila STARR-seq vectors carried either DSCP developmental or Rps12 housekeeping core promoters. The 249-bp inserts were synthesized with cloning adapters, and reporter RNA and plasmid DNA input were mapped exactly to wild-type or mutant reference oligos and collapsed by 10-bp UMIs. DESeq2 log2 fold-change activity values were calculated separately for each promoter using three biological replicates, one-read pseudocounts for zero RNA counts, and wild-type negative-region counts as inter-sample scaling factors.

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 · 35 definitions

oligo_id: Unique identifier for the synthesized oligo construct.
sequence_id: Parent genomic enhancer or 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 wt, motif mutagenesis, flank importance, shuffle bins, or synthetic enhancers.
sequence: 249-bp enhancer or control sequence inserted into the STARR-seq reporter, without constant cloning linkers.
enhancer_type: Author-provided Drosophila enhancer/control class.
motif_mutated: Motif or control sequence targeted by the mutation; NA for constructs without a motif mutation.
mutant_version: Identifier for the shuffled motif version used in a mutant construct.
copy_paste_wt_enhancer: Wild-type enhancer identifier for copy/paste flank constructs, when applicable.
copy_paste_flank_size: Flanking sequence size used in a copy/paste construct, when applicable.
copy_paste_imp_cutoff: DeepSTARR importance cutoff used to select a copy/paste construct, when supplied.
copy_paste_type: Copy/paste construct subtype, when applicable.
input_dev_rep1_umi: Developmental-screen replicate 1 plasmid DNA input UMI count.
input_dev_rep2_umi: Developmental-screen replicate 2 plasmid DNA input UMI count.
input_dev_rep3_umi: Developmental-screen replicate 3 plasmid DNA input UMI count.
input_hk_rep1_umi: Housekeeping-screen replicate 1 plasmid DNA input UMI count.
input_hk_rep2_umi: Housekeeping-screen replicate 2 plasmid DNA input UMI count.
input_hk_rep3_umi: Housekeeping-screen replicate 3 plasmid DNA input UMI count.
starrseq_dev_rep1_umi: Developmental-screen replicate 1 reporter-RNA UMI count.
starrseq_dev_rep2_umi: Developmental-screen replicate 2 reporter-RNA UMI count.
starrseq_dev_rep3_umi: Developmental-screen replicate 3 reporter-RNA UMI count.
starrseq_hk_rep1_umi: Housekeeping-screen replicate 1 reporter-RNA UMI count.
starrseq_hk_rep2_umi: Housekeeping-screen replicate 2 reporter-RNA UMI count.
starrseq_hk_rep3_umi: Housekeeping-screen replicate 3 reporter-RNA UMI count.
dev_base_mean: DESeq2 mean normalized count for the developmental screen.
dev_log2_fold_change: DESeq2 log2 reporter-RNA versus plasmid-input activity for the developmental screen.
dev_p_value: DESeq2 p-value for developmental reporter activity versus input.
dev_padj: Benjamini-Hochberg adjusted DESeq2 p-value for developmental activity.
hk_base_mean: DESeq2 mean normalized count for the housekeeping screen.
hk_log2_fold_change: DESeq2 log2 reporter-RNA versus plasmid-input activity for the housekeeping screen.
hk_p_value: DESeq2 p-value for housekeeping reporter activity versus input.
hk_padj: Benjamini-Hochberg adjusted DESeq2 p-value for housekeeping activity.
dev_qc_pass: TRUE when all three developmental-screen input replicates have at least 10 UMI reads.
hk_qc_pass: TRUE when all three housekeeping-screen input replicates have at least 10 UMI reads.
qc_pass: TRUE when the oligo passes the input threshold for at least one promoter screen and has an author-supplied activity result.

Quality control

The authors retained oligo reads with correct length and strand and no mapping mismatches after UMI collapsing. For each promoter screen, oligos were required to have at least 10 UMI reads in every input replicate; zero RNA counts received a one-read pseudocount, and activity was estimated with DESeq2 using negative-region scaling. The processed table retains rows passing the input threshold for at least one screen and with author-supplied activity results: 23,571 rows total, including 23,333 developmental-screen passes and 23,463 housekeeping-screen passes; screen-specific values are NA when that screen failed its input filter.

Curation notes

The GEO count matrix contains 23,959 Drosophila oligos; the author-provided final figure table retained here contains 23,571 rows after removing constructs with no screen passing the input/activity criteria and adds DESeq2 statistics. The final table includes 243 Med14_enhancers_shuffle_bins constructs not described in the concise GEO summary, so they were retained as a documented library component. Generic S2 was mapped to canonical Schneider 2 (CVCL:Z232) because the exact isolate is not stated.

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