Experiment / E4N6QMVOZEpisomal Plasmid MPRA

Dose-response episomal MPRA: 0–64 µM forskolin

Dissection of c-AMP Response Element Architecture by Using Genomic and Episomal Massively Parallel Reporter Assays

SP3 and SP5 synthetic CRE libraries were assayed episomally across nine forskolin concentrations, with two biological replicates per condition.

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:0063
Reference genome: GRCh38
Design focus: Synthetic / Motif-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

0, 1, 2, 4, 8, 16, 25, 32, or 64 µM forskolin for 3 h

Synthetic 150-bp cis-regulatory elements were placed upstream of a minimal promoter/luciferase reporter and associated with random 20-nt barcodes; element activity is summarized from barcode RNA/DNA ratios after forskolin treatment.

Processed data

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

Search table valuesFilter columnOperatorValue

Visible columns (137 of 137)

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 · 137 definitions

element_id: Stable identifier assigned to the unique tested element in this packaged library.
library_subpool: Source library subpool or follow-up design family.
design_library: Design family encoded by the paper/GEO element name.
element_name: Original construct name from the GEO barcode-variant mapping table.
element_sequence: 5-prime-to-3-prime variant sequence after reverse-complementing the sequencing-oriented mapping sequence.
sequence_length_bp: Length of the reported variant sequence in base pairs.
background_id: Paper background identifier used for background normalization when available.
site_configuration: Compact interpretation of the CRE-site or background design.
cre_site_1: State of CRE site 1 (consensus, weak, or no_site) when encoded by the construct name.
cre_site_2: State of CRE site 2 (consensus, weak, or no_site) when encoded by the construct name.
cre_site_3: State of CRE site 3 (consensus, weak, or no_site) when encoded by the construct name.
cre_site_4: State of CRE site 4 (consensus, weak, or no_site) when encoded by the construct name.
cre_site_5: State of CRE site 5 (consensus, weak, or no_site) when encoded by the construct name.
cre_site_6: State of CRE site 6 (consensus, weak, or no_site) when encoded by the construct name.
cre_spacing_bp: CRE-to-CRE spacing in base pairs when encoded by the design.
cre_distance_bp: CRE-to-promoter distance in base pairs when encoded by the design.
scramble_distance_bp: Distance of a 10-bp background scramble from the promoter in base pairs.
scramble_similarity: Per-position similarity score of a background scramble to its original background.
dna_barcode_count: Number of mapped barcodes passing the DNA read threshold for the element.
dna_read_sum: Sum of raw DNA barcode reads for barcodes passing the DNA read threshold.
activity_0uM_repA: Median barcode RNA/DNA activity ratio after per-sample normalization to one million total reads, for the named condition/replicate or its mean.
activity_0uM_repB: Median barcode RNA/DNA activity ratio after per-sample normalization to one million total reads, for the named condition/replicate or its mean.
activity_0uM_mean: Median barcode RNA/DNA activity ratio after per-sample normalization to one million total reads, for the named condition/replicate or its mean.
mad_0uM_repA: Median absolute deviation of barcode-level RNA/DNA activity ratios for the named condition and replicate.
mad_0uM_repB: Median absolute deviation of barcode-level RNA/DNA activity ratios for the named condition and replicate.
rna_barcodes_0uM_repA: Number of retained DNA-qualified barcodes with nonzero RNA reads in the named condition and replicate.
rna_barcodes_0uM_repB: Number of retained DNA-qualified barcodes with nonzero RNA reads in the named condition and replicate.
activity_1uM_repA: Median barcode RNA/DNA activity ratio after per-sample normalization to one million total reads, for the named condition/replicate or its mean.
activity_1uM_repB: Median barcode RNA/DNA activity ratio after per-sample normalization to one million total reads, for the named condition/replicate or its mean.
activity_1uM_mean: Median barcode RNA/DNA activity ratio after per-sample normalization to one million total reads, for the named condition/replicate or its mean.
mad_1uM_repA: Median absolute deviation of barcode-level RNA/DNA activity ratios for the named condition and replicate.
mad_1uM_repB: Median absolute deviation of barcode-level RNA/DNA activity ratios for the named condition and replicate.
rna_barcodes_1uM_repA: Number of retained DNA-qualified barcodes with nonzero RNA reads in the named condition and replicate.
rna_barcodes_1uM_repB: Number of retained DNA-qualified barcodes with nonzero RNA reads in the named condition and replicate.
activity_2uM_repA: Median barcode RNA/DNA activity ratio after per-sample normalization to one million total reads, for the named condition/replicate or its mean.
activity_2uM_repB: Median barcode RNA/DNA activity ratio after per-sample normalization to one million total reads, for the named condition/replicate or its mean.
activity_2uM_mean: Median barcode RNA/DNA activity ratio after per-sample normalization to one million total reads, for the named condition/replicate or its mean.
mad_2uM_repA: Median absolute deviation of barcode-level RNA/DNA activity ratios for the named condition and replicate.
mad_2uM_repB: Median absolute deviation of barcode-level RNA/DNA activity ratios for the named condition and replicate.
rna_barcodes_2uM_repA: Number of retained DNA-qualified barcodes with nonzero RNA reads in the named condition and replicate.
rna_barcodes_2uM_repB: Number of retained DNA-qualified barcodes with nonzero RNA reads in the named condition and replicate.
activity_4uM_repA: Median barcode RNA/DNA activity ratio after per-sample normalization to one million total reads, for the named condition/replicate or its mean.
activity_4uM_repB: Median barcode RNA/DNA activity ratio after per-sample normalization to one million total reads, for the named condition/replicate or its mean.
activity_4uM_mean: Median barcode RNA/DNA activity ratio after per-sample normalization to one million total reads, for the named condition/replicate or its mean.
mad_4uM_repA: Median absolute deviation of barcode-level RNA/DNA activity ratios for the named condition and replicate.
mad_4uM_repB: Median absolute deviation of barcode-level RNA/DNA activity ratios for the named condition and replicate.
rna_barcodes_4uM_repA: Number of retained DNA-qualified barcodes with nonzero RNA reads in the named condition and replicate.
rna_barcodes_4uM_repB: Number of retained DNA-qualified barcodes with nonzero RNA reads in the named condition and replicate.
activity_8uM_repA: Median barcode RNA/DNA activity ratio after per-sample normalization to one million total reads, for the named condition/replicate or its mean.
activity_8uM_repB: Median barcode RNA/DNA activity ratio after per-sample normalization to one million total reads, for the named condition/replicate or its mean.
activity_8uM_mean: Median barcode RNA/DNA activity ratio after per-sample normalization to one million total reads, for the named condition/replicate or its mean.
mad_8uM_repA: Median absolute deviation of barcode-level RNA/DNA activity ratios for the named condition and replicate.
mad_8uM_repB: Median absolute deviation of barcode-level RNA/DNA activity ratios for the named condition and replicate.
rna_barcodes_8uM_repA: Number of retained DNA-qualified barcodes with nonzero RNA reads in the named condition and replicate.
rna_barcodes_8uM_repB: Number of retained DNA-qualified barcodes with nonzero RNA reads in the named condition and replicate.
activity_16uM_repA: Median barcode RNA/DNA activity ratio after per-sample normalization to one million total reads, for the named condition/replicate or its mean.
activity_16uM_repB: Median barcode RNA/DNA activity ratio after per-sample normalization to one million total reads, for the named condition/replicate or its mean.
activity_16uM_mean: Median barcode RNA/DNA activity ratio after per-sample normalization to one million total reads, for the named condition/replicate or its mean.
mad_16uM_repA: Median absolute deviation of barcode-level RNA/DNA activity ratios for the named condition and replicate.
mad_16uM_repB: Median absolute deviation of barcode-level RNA/DNA activity ratios for the named condition and replicate.
rna_barcodes_16uM_repA: Number of retained DNA-qualified barcodes with nonzero RNA reads in the named condition and replicate.
rna_barcodes_16uM_repB: Number of retained DNA-qualified barcodes with nonzero RNA reads in the named condition and replicate.
activity_25uM_repA: Median barcode RNA/DNA activity ratio after per-sample normalization to one million total reads, for the named condition/replicate or its mean.
activity_25uM_repB: Median barcode RNA/DNA activity ratio after per-sample normalization to one million total reads, for the named condition/replicate or its mean.
activity_25uM_mean: Median barcode RNA/DNA activity ratio after per-sample normalization to one million total reads, for the named condition/replicate or its mean.
mad_25uM_repA: Median absolute deviation of barcode-level RNA/DNA activity ratios for the named condition and replicate.
mad_25uM_repB: Median absolute deviation of barcode-level RNA/DNA activity ratios for the named condition and replicate.
rna_barcodes_25uM_repA: Number of retained DNA-qualified barcodes with nonzero RNA reads in the named condition and replicate.
rna_barcodes_25uM_repB: Number of retained DNA-qualified barcodes with nonzero RNA reads in the named condition and replicate.
activity_32uM_repA: Median barcode RNA/DNA activity ratio after per-sample normalization to one million total reads, for the named condition/replicate or its mean.
activity_32uM_repB: Median barcode RNA/DNA activity ratio after per-sample normalization to one million total reads, for the named condition/replicate or its mean.
activity_32uM_mean: Median barcode RNA/DNA activity ratio after per-sample normalization to one million total reads, for the named condition/replicate or its mean.
mad_32uM_repA: Median absolute deviation of barcode-level RNA/DNA activity ratios for the named condition and replicate.
mad_32uM_repB: Median absolute deviation of barcode-level RNA/DNA activity ratios for the named condition and replicate.
rna_barcodes_32uM_repA: Number of retained DNA-qualified barcodes with nonzero RNA reads in the named condition and replicate.
rna_barcodes_32uM_repB: Number of retained DNA-qualified barcodes with nonzero RNA reads in the named condition and replicate.
activity_64uM_repA: Median barcode RNA/DNA activity ratio after per-sample normalization to one million total reads, for the named condition/replicate or its mean.
activity_64uM_repB: Median barcode RNA/DNA activity ratio after per-sample normalization to one million total reads, for the named condition/replicate or its mean.
activity_64uM_mean: Median barcode RNA/DNA activity ratio after per-sample normalization to one million total reads, for the named condition/replicate or its mean.
mad_64uM_repA: Median absolute deviation of barcode-level RNA/DNA activity ratios for the named condition and replicate.
mad_64uM_repB: Median absolute deviation of barcode-level RNA/DNA activity ratios for the named condition and replicate.
rna_barcodes_64uM_repA: Number of retained DNA-qualified barcodes with nonzero RNA reads in the named condition and replicate.
rna_barcodes_64uM_repB: Number of retained DNA-qualified barcodes with nonzero RNA reads in the named condition and replicate.
log2_activity_0uM_mean: Base-2 logarithm of the element-level mean RNA/DNA activity ratio for the named condition.
log2_induction_0uM_vs_0uM: Base-2 log induction relative to the baseline condition, using the element-level mean activity ratios.
log2_activity_1uM_mean: Base-2 logarithm of the element-level mean RNA/DNA activity ratio for the named condition.
log2_induction_1uM_vs_0uM: Base-2 log induction relative to the baseline condition, using the element-level mean activity ratios.
log2_activity_2uM_mean: Base-2 logarithm of the element-level mean RNA/DNA activity ratio for the named condition.
log2_induction_2uM_vs_0uM: Base-2 log induction relative to the baseline condition, using the element-level mean activity ratios.
log2_activity_4uM_mean: Base-2 logarithm of the element-level mean RNA/DNA activity ratio for the named condition.
log2_induction_4uM_vs_0uM: Base-2 log induction relative to the baseline condition, using the element-level mean activity ratios.
log2_activity_8uM_mean: Base-2 logarithm of the element-level mean RNA/DNA activity ratio for the named condition.
log2_induction_8uM_vs_0uM: Base-2 log induction relative to the baseline condition, using the element-level mean activity ratios.
log2_activity_16uM_mean: Base-2 logarithm of the element-level mean RNA/DNA activity ratio for the named condition.
log2_induction_16uM_vs_0uM: Base-2 log induction relative to the baseline condition, using the element-level mean activity ratios.
log2_activity_25uM_mean: Base-2 logarithm of the element-level mean RNA/DNA activity ratio for the named condition.
log2_induction_25uM_vs_0uM: Base-2 log induction relative to the baseline condition, using the element-level mean activity ratios.
log2_activity_32uM_mean: Base-2 logarithm of the element-level mean RNA/DNA activity ratio for the named condition.
log2_induction_32uM_vs_0uM: Base-2 log induction relative to the baseline condition, using the element-level mean activity ratios.
log2_activity_64uM_mean: Base-2 logarithm of the element-level mean RNA/DNA activity ratio for the named condition.
log2_induction_64uM_vs_0uM: Base-2 log induction relative to the baseline condition, using the element-level mean activity ratios.
background_normalized_activity_0uM_repA: Activity ratio normalized within replicate to the matching no-CRE background element.
background_normalized_activity_0uM_repB: Activity ratio normalized within replicate to the matching no-CRE background element.
background_normalized_activity_0uM_mean: Activity ratio normalized within replicate to the matching no-CRE background element.
background_normalized_log2_activity_0uM_mean: Base-2 logarithm of mean activity normalized within replicate to the matching no-CRE background.
background_normalized_activity_1uM_repA: Activity ratio normalized within replicate to the matching no-CRE background element.
background_normalized_activity_1uM_repB: Activity ratio normalized within replicate to the matching no-CRE background element.
background_normalized_activity_1uM_mean: Activity ratio normalized within replicate to the matching no-CRE background element.
background_normalized_log2_activity_1uM_mean: Base-2 logarithm of mean activity normalized within replicate to the matching no-CRE background.
background_normalized_activity_2uM_repA: Activity ratio normalized within replicate to the matching no-CRE background element.
background_normalized_activity_2uM_repB: Activity ratio normalized within replicate to the matching no-CRE background element.
background_normalized_activity_2uM_mean: Activity ratio normalized within replicate to the matching no-CRE background element.
background_normalized_log2_activity_2uM_mean: Base-2 logarithm of mean activity normalized within replicate to the matching no-CRE background.
background_normalized_activity_4uM_repA: Activity ratio normalized within replicate to the matching no-CRE background element.
background_normalized_activity_4uM_repB: Activity ratio normalized within replicate to the matching no-CRE background element.
background_normalized_activity_4uM_mean: Activity ratio normalized within replicate to the matching no-CRE background element.
background_normalized_log2_activity_4uM_mean: Base-2 logarithm of mean activity normalized within replicate to the matching no-CRE background.
background_normalized_activity_8uM_repA: Activity ratio normalized within replicate to the matching no-CRE background element.
background_normalized_activity_8uM_repB: Activity ratio normalized within replicate to the matching no-CRE background element.
background_normalized_activity_8uM_mean: Activity ratio normalized within replicate to the matching no-CRE background element.
background_normalized_log2_activity_8uM_mean: Base-2 logarithm of mean activity normalized within replicate to the matching no-CRE background.
background_normalized_activity_16uM_repA: Activity ratio normalized within replicate to the matching no-CRE background element.
background_normalized_activity_16uM_repB: Activity ratio normalized within replicate to the matching no-CRE background element.
background_normalized_activity_16uM_mean: Activity ratio normalized within replicate to the matching no-CRE background element.
background_normalized_log2_activity_16uM_mean: Base-2 logarithm of mean activity normalized within replicate to the matching no-CRE background.
background_normalized_activity_25uM_repA: Activity ratio normalized within replicate to the matching no-CRE background element.
background_normalized_activity_25uM_repB: Activity ratio normalized within replicate to the matching no-CRE background element.
background_normalized_activity_25uM_mean: Activity ratio normalized within replicate to the matching no-CRE background element.
background_normalized_log2_activity_25uM_mean: Base-2 logarithm of mean activity normalized within replicate to the matching no-CRE background.
background_normalized_activity_32uM_repA: Activity ratio normalized within replicate to the matching no-CRE background element.
background_normalized_activity_32uM_repB: Activity ratio normalized within replicate to the matching no-CRE background element.
background_normalized_activity_32uM_mean: Activity ratio normalized within replicate to the matching no-CRE background element.
background_normalized_log2_activity_32uM_mean: Base-2 logarithm of mean activity normalized within replicate to the matching no-CRE background.
background_normalized_activity_64uM_repA: Activity ratio normalized within replicate to the matching no-CRE background element.
background_normalized_activity_64uM_repB: Activity ratio normalized within replicate to the matching no-CRE background element.
background_normalized_activity_64uM_mean: Activity ratio normalized within replicate to the matching no-CRE background element.
background_normalized_log2_activity_64uM_mean: Base-2 logarithm of mean activity normalized within replicate to the matching no-CRE background.

Quality control

Barcode DNA read count >6, more than 7 DNA-qualified barcodes per element, and positive element median activity in every condition and replicate; RNA/DNA counts were normalized per sample to one million reads.

Curation notes

The run-specific R analysis explicitly filters the barcode map to subpool 3, subpool 5, and controls. Packaged 4179 retained elements from 724667 mapped barcodes; activity is an element-level median over barcode ratios.

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

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

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