The follow-up SP5-derived library tests six-site CRE configurations, two-site spacing/distance variants, and 10-bp background scrambles in an episomal MPRA with two biological replicates at baseline and 4 µM forskolin.
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 or 4 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.
Visible columns (46 of 46)
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 · 46 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_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.
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_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.
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_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.
Quality control
Barcode DNA read count >6, more than 7 DNA-qualified barcodes per element, and positive element median activity in both replicates and both conditions; RNA/DNA counts were normalized per sample to one million reads.
Curation notes
The follow-up barcode statistics table is the study's dedicated mapping source; its most_common sequences were reverse-complemented to report the designed 5-prime-to-3-prime orientation. Packaged 13757 retained elements from 1172832 mapped barcodes; activity is an element-level median over barcode ratios.