The 5-bp synthetic STARR-seq library was integrated by Cre-recombinase cassette exchange into an AXIN2 landing pad in MEC-1 cells. The table summarizes QC-filtered construct-level gDNA-normalized mRNA activity, expression fraction, coverage, and no-TFBS-relative 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:1870
Reference genome
Not reported / not applicable
Design focus
Synthetic / Motif-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Basal / Untreated
Custom genome-integrated STARR-seq: loxP/lox2272-flanked origin/polyA and Cre-mediated cassette exchange into an AXIN2 landing pad in a stable MEC1-CRE landing-pad line; three gDNA and three mRNA replicates were read out after RPM normalization. Endogenous activity is mean mRNA/gDNA, and the derived no-TFBS-relative value subtracts the mean activity of rd control constructs.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (24 of 24)
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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 · 24 definitions
element_id
Full identifier for the synthetic sequence construct.
motif_syntax
Base TF motif syntax, excluding the sequence-context suffix.
sequence_context_id
Random sequence-context identifier used to embed the motif syntax.
sequence
Synthetic integrated STARR-seq insert sequence.
spacer_bp
Designed base-pair spacing between adjacent motif instances.
num_of_motifs
Number of TF motif instances, derived from the base syntax; rd controls are zero.
homotypic
Whether the construct uses one repeated TF motif rather than a mixed syntax, derived from the base syntax.
tf_first
First TF in the motif syntax.
tf_second
Second TF in the motif syntax when present.
motif_class_composition
Semicolon-delimited context/initiator class labels assigned to the TFs.
n_barcodes_qc
Number of barcode observations retained for the construct.
n_expressed_barcodes
Number of retained barcodes with positive average mRNA signal.
fraction_expressed_barcodes
Fraction of retained construct barcodes with positive average mRNA signal.
mean_rna_over_gdna
Mean barcode-level mRNA/gDNA activity across the three replicate pairs.
mean_rna_over_gdna_minus_noTFBS
Mean mRNA/gDNA activity after subtracting the rd no-TFBS control mean.
mean_gDNA_rpm
Mean read-depth-normalized gDNA count across retained barcodes.
median_gDNA_rpm
Median read-depth-normalized gDNA count across retained barcodes.
mean_mRNA_rpm
Mean read-depth-normalized mRNA count across retained barcodes.
mean_mapping_count
Mean barcode-to-fragment mapping count among retained observations.
fragment_qc_n_barcodes
Number of barcodes pooled across contexts for the fragment-level QC decision.
fragment_qc_n_expressed_barcodes
Number of expressed barcodes pooled across contexts for fragment-level QC.
fragment_qc_pass
Whether the base syntax passed the >=10 expressed-barcode filter.
gDNA_replicates_passing
Number of gDNA replicates meeting the source coverage requirement.
qc_pass
True for construct rows belonging to a fragment that passed the documented QC.
Quality control
Used the authors’ post-filtered barcode table; required n_gDNA_replicated_ov10 >=3 and average gDNA coverage >0, then retained only synthetic base syntaxes with >=10 unique expressed barcodes (average mRNA >0) pooled across the three sequence contexts, mirroring the authors’ fragment-level filter. Top-5% activity-outlier removal and barcode gDNA RPM thresholding were already applied in the source processed file; no additional rows from that stage were reintroduced. No-TFBS-relative activity is mean activity minus the rd-control mean (0.6398398027).
Curation notes
The table contains 445 construct rows from 150 passing base syntaxes. The source has 16,189 barcode rows and 185 base syntaxes, with 37 failing the >=10 expressed-barcode fragment QC. The endogenous source table already includes the authors’ post-filtered barcode-level activity and is not a raw read file.