A synthetic library of 6,600 nominal cis-regulatory elements combined CRX, NRL, NEUROD1, RORB, and MAZ binding-site building blocks to test motif diversity and cis-regulatory grammar. Barcoded plasmids were electroporated into P0 CD-1 mouse retinal explants in three replicate experiments, with reporter RNA/cDNA activity normalized to the input plasmid DNA library.
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.
Custom oligonucleotide CREs were cloned into pJK03 with the rod-specific Rho basal promoter, DsRed reporter, multiplexing barcode, and construct barcode. Each synthetic CRE was designed with three unique barcodes; two multiplexing-barcode sublibraries were pooled, electroporated into retinal explants, and measured by paired Illumina NextSeq RNA/cDNA and input-plasmid DNA sequencing. The published processed activity is the replicate-averaged log2 RNA/DNA score normalized to the Rho basal promoter.
Processed data
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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 · 14 definitions
element_id
Unique synthetic CDNRM CRE identifier from the published processed activity file and matching FASTA record.
sequence
100-bp synthetic CRE sequence consisting of five 20-bp motif building blocks; the Rho promoter, reporter, and barcodes are not included.
sequence_length_bp
Length of the synthetic CRE sequence in base pairs.
motif_arrangement
Compact paper/repository token order, for example ChChChDhMm; the first character identifies the TF and the second character identifies affinity.
tfbs_order
Expanded motif order with TF and affinity labels, separated by vertical bars; h=high, m=medium, and l=low affinity.
design_class
Synthetic library composition class: 3-1-1 means three CRX sites plus one site for each of two other TFs; 2-2-1 means two CRX sites, two sites for a second TF, and one site for a third TF.
crx_site_count
Number of CRX binding-site building blocks in the element.
crx_affinity_profile
Ordered affinities of CRX sites in the element, separated by vertical bars.
nrl_site_count
Number of NRL binding-site building blocks in the element.
neurod1_site_count
Number of NEUROD1 binding-site building blocks in the element.
rorb_site_count
Number of RORB binding-site building blocks in the element.
maz_site_count
Number of MAZ binding-site building blocks in the element.
other_tf_site_count
Number of non-CRX TF binding-site building blocks in the element.
mpra_log2_activity
Published mean log2 MPRA activity: RNA/DNA reporter signal after barcode and replicate aggregation and normalization to the Rho basal promoter.
Quality control
The paper processed all reads regardless of base-quality score, retained only exact barcode matches (95% of reads after filtering), removed barcodes with fewer than 50 input-plasmid/DNA reads, normalized barcode counts to reads per million, calculated RNA/DNA activity for each replicate, averaged across barcodes and the three replicate electroporations, normalized to the basal promoter, and log2-transformed the final activity. For this package, the 6,598 published building-block activity rows were required to have exactly one matching 100-bp FASTA sequence, valid A/C/G/T sequence content, a valid five-token motif arrangement, and a finite activity value; all rows passed these checks and no missing nominal elements were imputed.
Curation notes
This is the new CDNRM MPRA performed for the paper. The paper and GEO describe a nominal 6,600-element library, but the public processed activity file and sequence FASTA each contain 6,598 unique building-block elements; the two absent nominal elements were not reconstructed. The methods describe 20 genomic standards and 150 scrambled negative controls, but those controls are not present in the published building-block activity/FASTA files used here and were not fabricated. The retained barcode FASTA contains 3,300 building-block identifiers with three barcodes each plus 90 BASAL records, so it is preserved as source material but was not used to remove aggregate activity rows. The prior CRX+NRL synthetic MPRA and genomic retinal MPRA tables used for reanalysis are retained in raw_data only and are not represented as additional experiments here. The CDNRM sequences are synthetic motif constructs rather than genomic variants, so no reference assembly or continuous genomic region applies.