A library of overlapping 139-bp tiles from CREBBP-bound mouse distal enhancers and promoters, with human ortholog controls, was tested in matched enhancer and promoter MPRA reporters. The library was assayed in unstimulated neurons and after KCl depolarization with two biological replicates per condition.
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,hg19
Design focus
Region-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. The enhancer construct used a basal human FOS promoter and amplified the tile-containing reporter transcript; the promoter construct placed the tested tile upstream of GFP with a barcode in the 3-prime UTR. DNA/plasmid and cDNA barcode counts were obtained by high-throughput sequencing.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (56 of 56)
Row
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
Page 1 · 50 rows · More results available
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.
sequence
Representative mapped sequence from the deposited key/tally; for TN03/TN05 it is the highest-support observed tile sequence.
sequence_length
Length in nucleotides of the representative mapped sequence.
species
Species encoded by the deposited label (mouse or human ortholog).
reference_assembly
Reference genome assembly associated with the mapped sequence.
chromosome
Chromosome parsed from the deposited genomic label.
position
Genomic coordinate parsed from the deposited label; this is the labeled tile/locus coordinate, not a complete interval.
locus_id
Study-defined numeric locus or construct coordinate identifier parsed from the label.
tile_offset
Tile center offset relative to the locus peak used in the TN03 sliding genomic library.
motif_annotations
Motif calls or motif mutation annotations encoded in the original label.
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.
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.
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.
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.
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 TN03 tally is a legacy partial spreadsheet rather than the complete key-file barcode universe. The table retains mouse and human-ortholog tile labels and their representative mapped sequences; region_of_interest is null because loci are scattered genome-wide. GEO TN03 and TN05 tally supplements are legacy .xls files with a 65,535-row spreadsheet limit, while their deposited key files contain more barcode assignments; processed tables aggregate the deposited tally rows only. Duplicate (barcode, label) records were collapsed, barcodes assigned to multiple labels were excluded, and the >=20-read filter was applied after element-level aggregation. Raw SRA read files were not packaged because GEO lists approximately 47.9 GB of runs. Processed output contains 4397 QC-passing elements and 17 QC-passing negative-control elements.