CAD neuronal cell line 3′UTR RNA-localization MPRA

A plasmid reporter library containing 150-nt native mouse 3′UTR tiles and designed motif or synthetic-sequence variants was transfected into differentiated CAD cells grown on 3-µm transwell inserts. Soma and neurite fractions were collected after transfection and profiled in three biological replicates each using UMI-based targeted reporter sequencing.

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: Mouse
Taxonomy ID: NCBITaxon:10090
Biosample: CVCL:0199
Reference genome: mm10
Design focus: Region-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / untreated after serum-starvation differentiation

CMV promoter → eGFP → 12-nt barcode → 150-nt 3′UTR test sequence → polyadenylation site; 198-nt oligos were cloned into a pcDNA3-EGFP-derived episomal reporter. Soma and neurite RNA were separated on transwell inserts and measured by targeted cDNA sequencing with 15-nt UMIs; the primary readout is edgeR log2 fold-change for neurite versus soma abundance.

Quality control

Author QC was retained: reporter reads were assigned by a unique 12-nt barcode and collapsed to UMI counts, and edgeR likelihood-ratio-test log2 fold-changes and p-values were used for enrichment. The processed table keeps only variants with a nonzero UMI count in each of the six CAD soma/neurite libraries (42,062 of 47,347 Supplementary Table S2 variants, matching the count-availability number reported in the paper). Localization calls are derived as neurite- or soma-enriched when the corresponding published p-value is <0.05 and the log2 fold-change has the matching sign; all retained rows are marked qc_pass=true.

Curation notes

CAD and Neuro-2a were parallel cell-line arms of the same reporter-library study and are represented as separate child experiments so each record has one Cellosaurus biosample. This table retains all distinct barcoded library variants passing the count-availability filter, including the native 3′UTR tiles and designed motif/synthetic sublibraries; it does not collapse repeated sequences with different barcodes. The reference genome is recorded as mm10 because the Supplementary Table S1 mouse coordinates match the mm10/GRCm38 assembly, although the article does not print an assembly label. The original GEO file contains 642 additional barcode-only records without Supplementary Table S2 annotations; they are retained in raw_data but excluded here.

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CAD neuronal cell line 3′UTR RNA-localization MPRA

Processed data

Quality control

Curation notes

Cite OpenMPRA

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