Experiment / E6D22FC11Standard STARR-seq

GP5d random-enhancer STARR-seq

Sequence determinants of human gene regulatory elements

A random N170 enhancer library was assayed in GP5d cells in two biological replicates using STARR-seq. The table summarizes motif-match activity effects from both replicates and the corresponding HepG2 comparison output.

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:1235
Reference genome: Not reported / not applicable
Design focus: Synthetic / Motif-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated

Episomal pCpG-free-Sasaki-SS STARR-seq library containing synthetic random N170 enhancer sequences in the reporter 3′ UTR. GP5d RNA was collected 24 h after transfection; source motif matching used MOODS at p=1e-6 and the activity output is PsiLFC.

Processed data

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

Visible columns (17 of 17)

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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 · 17 definitions

motif_model: Position-frequency-matrix model name
tf: Transcription-factor label associated with the motif model
gp5d_rep1_total_match_count: GP5d replicate 1 total motif-match count in RNA
gp5d_rep1_input_match_count: GP5d replicate 1 input-DNA motif-match count
gp5d_rep1_log2_effect: GP5d replicate 1 PsiLFC/log2 RNA-over-input effect
gp5d_rep2_total_match_count: GP5d replicate 2 total motif-match count in RNA
gp5d_rep2_input_match_count: GP5d replicate 2 input-DNA motif-match count
gp5d_rep2_log2_effect: GP5d replicate 2 PsiLFC/log2 RNA-over-input effect
hepg2_total_match_count: HepG2 total motif-match count in RNA
hepg2_input_match_count: HepG2 input-DNA motif-match count
hepg2_log2_effect: HepG2 PsiLFC/log2 RNA-over-input effect
gp5d_mean_log2_effect: Mean GP5d log2 activity effect across two replicates
gp5d_replicate_sd: Sample standard deviation of the two GP5d replicate effects
hepg2_minus_gp5d_mean_log2_effect: HepG2 effect minus mean GP5d effect
gp5d_rep1_minus_rep2_effect: GP5d replicate 1 effect minus replicate 2 effect
motif_match_pvalue_threshold: MOODS motif-match p-value threshold used by the source
source_accessions: GEO accessions contributing to the row

Quality control

The GEO files contain 1,121 motif models per condition. Package QC required finite effects, nonnegative integer match counts, and total-plus-input counts of at least 5; all 1,121 common motif models were retained for the GP5d comparison.

Curation notes

The deposited random-enhancer files are motif-match aggregate outputs rather than sequence-level oligo counts; the HepG2 values are included as a comparison column while the experiment is anchored to the two GP5d replicates.

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