Synthetic motif and motif-spacing constructs were tested in matched enhancer and promoter MPRA reporters. The library was assayed in unstimulated neurons and after KCl depolarization with three biological replicates per condition; each labeled construct has multiple barcode observations in the deposited tally.
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
Mouse
Taxonomy ID
NCBITaxon:10090
Biosample
CL:0010012
Reference genome
mm9
Design focus
Synthetic / Motif-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Unstimulated or 55 mM KCl depolarization for 12 h
Ex vivo primary E16 CD-1 mouse cortical neurons were transduced with AAV1/AAV2 reporter libraries containing de novo motif combinations, motif spacings, and endogenous-background constructs. The tally supplement encodes construct designs in labels but does not provide a separate full synthetic oligo sequence column. DNA/plasmid and cDNA barcode counts were used for enhancer and promoter activity.
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 · 56 definitions
element_id
Stable identifier generated from the deposited construct or tile label.
source_label
Original sequence/construct label from the GEO tally supplement.
source_class
Library-defined class parsed from the original label.
is_negative_control
Whether the element was used as the negative-control class for activity normalization.
barcode_count
Number of unique deposited barcode records retained for this element after mapping cleanup.
qc_min_read_count
Minimum summed DNA or RNA read count across all samples represented in this table; all output rows meet the >=20-read QC threshold.
construct_annotation
Synthetic construct annotation following the first period in the TN04 label.
motif_name
Best-effort motif/design name parsed from the TN04 construct annotation.
motif_sequence_or_design
Deposited motif sequence or construct design string; the TN04 tally does not contain a separate full oligo-sequence column.
background_annotation
Background-sequence annotation parsed from TN04 labels containing an on_bkg field.
spacing_bp
Explicit motif spacing in base pairs when encoded in the TN04 label; otherwise blank.
source_data
GEO series and library tally source for the row.
dna_enhancer_count
Summed DNA/plasmid barcode count for the enhancer reporter library.
dna_promoter_count
Summed DNA/plasmid barcode count for the promoter reporter library.
enhancer_unstimulated_rep1_rna_count
Raw cDNA/RNA barcode count for the indicated reporter assay, condition, and biological replicate.
enhancer_unstimulated_rep2_rna_count
Raw cDNA/RNA barcode count for the indicated reporter assay, condition, and biological replicate.
enhancer_unstimulated_rep3_rna_count
Raw cDNA/RNA barcode count for the indicated reporter assay, condition, and biological replicate.
promoter_unstimulated_rep1_rna_count
Raw cDNA/RNA barcode count for the indicated reporter assay, condition, and biological replicate.
promoter_unstimulated_rep2_rna_count
Raw cDNA/RNA barcode count for the indicated reporter assay, condition, and biological replicate.
promoter_unstimulated_rep3_rna_count
Raw cDNA/RNA barcode count for the indicated reporter assay, condition, and biological replicate.
enhancer_kcl_rep1_rna_count
Raw cDNA/RNA barcode count for the indicated reporter assay, condition, and biological replicate.
enhancer_kcl_rep2_rna_count
Raw cDNA/RNA barcode count for the indicated reporter assay, condition, and biological replicate.
enhancer_kcl_rep3_rna_count
Raw cDNA/RNA barcode count for the indicated reporter assay, condition, and biological replicate.
promoter_kcl_rep1_rna_count
Raw cDNA/RNA barcode count for the indicated reporter assay, condition, and biological replicate.
promoter_kcl_rep2_rna_count
Raw cDNA/RNA barcode count for the indicated reporter assay, condition, and biological replicate.
promoter_kcl_rep3_rna_count
Raw cDNA/RNA barcode count for the indicated reporter assay, condition, and biological replicate.
enhancer_unstimulated_activity_fold
Mean per-replicate RNA/DNA ratio divided by the mean ratio of the library negative controls; activity fold relative to negative controls.
enhancer_unstimulated_log2_activity
Log2-transformed normalized MPRA activity fold relative to negative controls.
enhancer_unstimulated_log2_sd
Sample standard deviation across replicate-level log2 normalized activity values.
enhancer_unstimulated_replicate_n
Number of biological replicates contributing to the normalized activity value.
enhancer_unstimulated_pvalue
Empirical p-value: fraction of QC-passing negative-control elements with normalized activity at least as high as this element.
enhancer_unstimulated_fdr
Benjamini–Hochberg FDR-adjusted empirical p-value across QC-passing elements for this assay and condition.
promoter_unstimulated_activity_fold
Mean per-replicate RNA/DNA ratio divided by the mean ratio of the library negative controls; activity fold relative to negative controls.
promoter_unstimulated_log2_activity
Log2-transformed normalized MPRA activity fold relative to negative controls.
promoter_unstimulated_log2_sd
Sample standard deviation across replicate-level log2 normalized activity values.
promoter_unstimulated_replicate_n
Number of biological replicates contributing to the normalized activity value.
promoter_unstimulated_pvalue
Empirical p-value: fraction of QC-passing negative-control elements with normalized activity at least as high as this element.
promoter_unstimulated_fdr
Benjamini–Hochberg FDR-adjusted empirical p-value across QC-passing elements for this assay and condition.
enhancer_kcl_activity_fold
Mean per-replicate RNA/DNA ratio divided by the mean ratio of the library negative controls; activity fold relative to negative controls.
enhancer_kcl_log2_activity
Log2-transformed normalized MPRA activity fold relative to negative controls.
enhancer_kcl_log2_sd
Sample standard deviation across replicate-level log2 normalized activity values.
enhancer_kcl_replicate_n
Number of biological replicates contributing to the normalized activity value.
enhancer_kcl_pvalue
Empirical p-value: fraction of QC-passing negative-control elements with normalized activity at least as high as this element.
enhancer_kcl_fdr
Benjamini–Hochberg FDR-adjusted empirical p-value across QC-passing elements for this assay and condition.
promoter_kcl_activity_fold
Mean per-replicate RNA/DNA ratio divided by the mean ratio of the library negative controls; activity fold relative to negative controls.
promoter_kcl_log2_activity
Log2-transformed normalized MPRA activity fold relative to negative controls.
promoter_kcl_log2_sd
Sample standard deviation across replicate-level log2 normalized activity values.
promoter_kcl_replicate_n
Number of biological replicates contributing to the normalized activity value.
promoter_kcl_pvalue
Empirical p-value: fraction of QC-passing negative-control elements with normalized activity at least as high as this element.
promoter_kcl_fdr
Benjamini–Hochberg FDR-adjusted empirical p-value across QC-passing elements for this assay and condition.
enhancer_kcl_vs_unstimulated_log2
Change in enhancer log2 activity after KCl depolarization versus unstimulated neurons.
promoter_kcl_vs_unstimulated_log2
Change in promoter log2 activity after KCl depolarization versus unstimulated neurons.
max_enhancer_noDN_condition
Condition (unstimulated or KCl) with the highest enhancer activity, excluding TN05 DN conditions.
max_enhancer_noDN_log2_activity
Maximum enhancer log2 activity across unstimulated and KCl conditions, excluding TN05 DN conditions.
max_promoter_noDN_condition
Condition (unstimulated or KCl) with the highest promoter activity, excluding TN05 DN conditions.
max_promoter_noDN_log2_activity
Maximum promoter log2 activity across unstimulated and KCl conditions, excluding TN05 DN conditions.
Quality control
Applied the paper supplemental-methods QC: remove sequence tiles with fewer than 20 reads in any DNA/cDNA sample. Counts were aggregated at the labeled element after barcode mapping cleanup; normalized activity is the mean replicate RNA/DNA ratio divided by the mean ratio of QC-passing negative controls, reported as fold and log2 activity. Empirical p-values are the fraction of negative controls at or above each element, with Benjamini–Hochberg FDR correction.
Curation notes
The deposited TN04 tally contains 1,375 construct labels with nine barcode rows per label before QC. For MPRA normalization, the three deposited CREB_cntl_set.neg_CREBx4 controls were used as negative controls because they are explicit negative-control constructs in the tally and all pass the read-count filter. The exact top25_packed MYBL2 negative-control label fails the >=20-read threshold in the deposited tally and was excluded; the tally only supplies label-level synthetic design annotations, not a separate full sequence table. The construct set is synthetic/de novo, so region_of_interest is null. Processed output contains 1239 QC-passing elements and 3 QC-passing negative-control elements.