Main episomal MPRA: logarithmic forskolin dose series
Dissection of c-AMP Response Element Architecture by Using Genomic and Episomal Massively Parallel Reporter AssaysThe main SP3/SP5 episomal CRE library was measured in two biological replicates over a logarithmic forskolin series from baseline through 4 µM.
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Perturbation & assay details
0, 0.03125, 0.0625, 0.125, 0.25, 0.5, 1, 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
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Column dictionary · 124 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_0.03125uM_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_0.03125uM_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_0.03125uM_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_0.03125uM_repA
- Median absolute deviation of barcode-level RNA/DNA activity ratios for the named condition and replicate.
- mad_0.03125uM_repB
- Median absolute deviation of barcode-level RNA/DNA activity ratios for the named condition and replicate.
- rna_barcodes_0.03125uM_repA
- Number of retained DNA-qualified barcodes with nonzero RNA reads in the named condition and replicate.
- rna_barcodes_0.03125uM_repB
- Number of retained DNA-qualified barcodes with nonzero RNA reads in the named condition and replicate.
- activity_0.0625uM_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_0.0625uM_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_0.0625uM_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_0.0625uM_repA
- Median absolute deviation of barcode-level RNA/DNA activity ratios for the named condition and replicate.
- mad_0.0625uM_repB
- Median absolute deviation of barcode-level RNA/DNA activity ratios for the named condition and replicate.
- rna_barcodes_0.0625uM_repA
- Number of retained DNA-qualified barcodes with nonzero RNA reads in the named condition and replicate.
- rna_barcodes_0.0625uM_repB
- Number of retained DNA-qualified barcodes with nonzero RNA reads in the named condition and replicate.
- activity_0.125uM_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_0.125uM_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_0.125uM_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_0.125uM_repA
- Median absolute deviation of barcode-level RNA/DNA activity ratios for the named condition and replicate.
- mad_0.125uM_repB
- Median absolute deviation of barcode-level RNA/DNA activity ratios for the named condition and replicate.
- rna_barcodes_0.125uM_repA
- Number of retained DNA-qualified barcodes with nonzero RNA reads in the named condition and replicate.
- rna_barcodes_0.125uM_repB
- Number of retained DNA-qualified barcodes with nonzero RNA reads in the named condition and replicate.
- activity_0.25uM_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_0.25uM_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_0.25uM_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_0.25uM_repA
- Median absolute deviation of barcode-level RNA/DNA activity ratios for the named condition and replicate.
- mad_0.25uM_repB
- Median absolute deviation of barcode-level RNA/DNA activity ratios for the named condition and replicate.
- rna_barcodes_0.25uM_repA
- Number of retained DNA-qualified barcodes with nonzero RNA reads in the named condition and replicate.
- rna_barcodes_0.25uM_repB
- Number of retained DNA-qualified barcodes with nonzero RNA reads in the named condition and replicate.
- activity_0.5uM_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_0.5uM_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_0.5uM_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_0.5uM_repA
- Median absolute deviation of barcode-level RNA/DNA activity ratios for the named condition and replicate.
- mad_0.5uM_repB
- Median absolute deviation of barcode-level RNA/DNA activity ratios for the named condition and replicate.
- rna_barcodes_0.5uM_repA
- Number of retained DNA-qualified barcodes with nonzero RNA reads in the named condition and replicate.
- rna_barcodes_0.5uM_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_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_0.03125uM_mean
- Base-2 logarithm of the element-level mean RNA/DNA activity ratio for the named condition.
- log2_induction_0.03125uM_vs_0uM
- Base-2 log induction relative to the baseline condition, using the element-level mean activity ratios.
- log2_activity_0.0625uM_mean
- Base-2 logarithm of the element-level mean RNA/DNA activity ratio for the named condition.
- log2_induction_0.0625uM_vs_0uM
- Base-2 log induction relative to the baseline condition, using the element-level mean activity ratios.
- log2_activity_0.125uM_mean
- Base-2 logarithm of the element-level mean RNA/DNA activity ratio for the named condition.
- log2_induction_0.125uM_vs_0uM
- Base-2 log induction relative to the baseline condition, using the element-level mean activity ratios.
- log2_activity_0.25uM_mean
- Base-2 logarithm of the element-level mean RNA/DNA activity ratio for the named condition.
- log2_induction_0.25uM_vs_0uM
- Base-2 log induction relative to the baseline condition, using the element-level mean activity ratios.
- log2_activity_0.5uM_mean
- Base-2 logarithm of the element-level mean RNA/DNA activity ratio for the named condition.
- log2_induction_0.5uM_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_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_0.03125uM_repA
- Activity ratio normalized within replicate to the matching no-CRE background element.
- background_normalized_activity_0.03125uM_repB
- Activity ratio normalized within replicate to the matching no-CRE background element.
- background_normalized_activity_0.03125uM_mean
- Activity ratio normalized within replicate to the matching no-CRE background element.
- background_normalized_log2_activity_0.03125uM_mean
- Base-2 logarithm of mean activity normalized within replicate to the matching no-CRE background.
- background_normalized_activity_0.0625uM_repA
- Activity ratio normalized within replicate to the matching no-CRE background element.
- background_normalized_activity_0.0625uM_repB
- Activity ratio normalized within replicate to the matching no-CRE background element.
- background_normalized_activity_0.0625uM_mean
- Activity ratio normalized within replicate to the matching no-CRE background element.
- background_normalized_log2_activity_0.0625uM_mean
- Base-2 logarithm of mean activity normalized within replicate to the matching no-CRE background.
- background_normalized_activity_0.125uM_repA
- Activity ratio normalized within replicate to the matching no-CRE background element.
- background_normalized_activity_0.125uM_repB
- Activity ratio normalized within replicate to the matching no-CRE background element.
- background_normalized_activity_0.125uM_mean
- Activity ratio normalized within replicate to the matching no-CRE background element.
- background_normalized_log2_activity_0.125uM_mean
- Base-2 logarithm of mean activity normalized within replicate to the matching no-CRE background.
- background_normalized_activity_0.25uM_repA
- Activity ratio normalized within replicate to the matching no-CRE background element.
- background_normalized_activity_0.25uM_repB
- Activity ratio normalized within replicate to the matching no-CRE background element.
- background_normalized_activity_0.25uM_mean
- Activity ratio normalized within replicate to the matching no-CRE background element.
- background_normalized_log2_activity_0.25uM_mean
- Base-2 logarithm of mean activity normalized within replicate to the matching no-CRE background.
- background_normalized_activity_0.5uM_repA
- Activity ratio normalized within replicate to the matching no-CRE background element.
- background_normalized_activity_0.5uM_repB
- Activity ratio normalized within replicate to the matching no-CRE background element.
- background_normalized_activity_0.5uM_mean
- Activity ratio normalized within replicate to the matching no-CRE background element.
- background_normalized_log2_activity_0.5uM_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_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 every condition and replicate; RNA/DNA counts were normalized per sample to one million reads.
Curation notes
This is the main episomal run used by the repository's figure-generation script. Packaged 4186 retained elements from 724667 mapped barcodes; activity is an element-level median over barcode ratios.