Experiment / E0K9GDHVOTargeted Genomic Integration MPRA

Targeted genomic-integration MPRA at the H11 landing pad

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

The SP3/SP5 library was integrated into the defined H11 landing pad in HEK293T cells by BxB1 recombination and measured at 8 µM forskolin in two biological replicates, each with two DNA technical replicates.

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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

8 µM forskolin for 4 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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Visible columns (34 of 34)

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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 · 34 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_rep1: Number of mapped barcodes passing the DNA read threshold for the element.
dna_barcode_count_rep2: Number of mapped barcodes passing the DNA read threshold for the element.
dna_read_sum_rep1: Sum of raw DNA barcode reads for barcodes passing the DNA read threshold.
dna_read_sum_rep2: Sum of raw DNA barcode reads for barcodes passing the DNA read threshold.
activity_8uM_rep1: 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_rep2: 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_rep1: Median absolute deviation of barcode-level RNA/DNA activity ratios for the named condition and replicate.
mad_8uM_rep2: Median absolute deviation of barcode-level RNA/DNA activity ratios for the named condition and replicate.
rna_barcodes_8uM_rep1: Number of retained DNA-qualified barcodes with nonzero RNA reads in the named condition and replicate.
rna_barcodes_8uM_rep2: Number of retained DNA-qualified barcodes with nonzero RNA reads in the named condition and replicate.
log2_activity_8uM_mean: Base-2 logarithm of the element-level mean RNA/DNA activity ratio for the named condition.
background_normalized_activity_8uM_rep1: Activity ratio normalized within replicate to the matching no-CRE background element.
background_normalized_activity_8uM_rep2: 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.

Quality control

Required >6 DNA reads in both technical DNA replicates, more than 7 barcodes per element in each biological replicate, and positive element median activity in both biological replicates; DNA technical replicates were averaged after per-sample one-million-read normalization.

Curation notes

The GEO sample titles and genomic R script identify the RNA condition as 8 µM forskolin; a prose methods line displays a conflicting value, so the accession/sample annotation and analysis code were followed. Packaged 3491 retained elements from 724667 mapped barcodes; activity is an element-level median over barcode ratios.

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