The shared synthetic 3′UTR reporter library was transfected into mouse Neuro-2a neuroblastoma cells, and one RNA output sample was barcode-sequenced against the two-replicate plasmid input 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.
Organism
Mouse
Taxonomy ID
NCBITaxon:10090
Biosample
CVCL:0470
Reference genome
Not reported / not applicable
Design focus
Synthetic / Motif-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Basal / Untreated
Episomal CMV/TO-EGFP reporter with 642 synthetic 3′UTR identities and co-transcribed 9-bp barcodes. The N2A sample measured reporter RNA abundance only; no polysome or 40S fraction was deposited for this cell-type comparison.
Processed data
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Column dictionary · 19 definitions
construct_id
Canonical synthetic 3′UTR reporter identity from the source library.
construct_class
Curated class of the reporter identity: blank control, synthetic element combination, let-7 variant, natural let-7 target, or let-7 copy-number variant.
element_position_1
Regulatory element at synthetic 3′UTR position 1; blank for special variant/natural-target identities whose positional encoding is not explicit in the identity label.
element_position_2
Regulatory element at synthetic 3′UTR position 2; blank for special variant/natural-target identities whose positional encoding is not explicit in the identity label.
element_position_3
Regulatory element at synthetic 3′UTR position 3; blank for special variant/natural-target identities whose positional encoding is not explicit in the identity label.
element_position_4
Regulatory element at synthetic 3′UTR position 4; blank for special variant/natural-target identities whose positional encoding is not explicit in the identity label.
regulatory_sequence
132-nt synthetic regulatory-element sequence from Supplementary Data 1, with source capitalization retained.
regulatory_sequence_length_nt
Length of the source regulatory-element sequence in nucleotides.
library_barcode_count
Number of distinct source barcodes assigned to this reporter identity.
qc_barcode_count
Number of barcodes retained after the package read-count QC filter.
plasmid_count_rep1_mean
Mean raw plasmid-input read count per QC-passing barcode in plasmid replicate 1.
plasmid_count_rep2_mean
Mean raw plasmid-input read count per QC-passing barcode in plasmid replicate 2.
cell_type
Source cell-type label for the RNA output sample.
rna_count_mean
Mean raw reporter RNA/cDNA read count per QC-passing barcode in the cell-type sample.
rna_activity_log2_median
Median barcode-level log2 reporter RNA/plasmid activity relative to the 4×blank (BBBB) control.
rna_activity_log2_mean
Arithmetic mean of barcode-level log2 reporter RNA/plasmid activity values.
rna_activity_log2_sd
Sample standard deviation of barcode-level log2 reporter RNA/plasmid activity values.
rna_activity_log2_observations
Number of QC-passing barcode observations contributing to the activity summary.
qc_pass
TRUE for reporter identities with at least three barcodes passing the package QC filter.
Quality control
The authors used >10-read barcode filtering for cDNA/plasmid pools and analyzed one biological replicate for non-HeLa cell types. The package required >10 counts in both plasmid replicates and the cell-type RNA sample, then retained reporter identities with at least three passing barcodes; all 642 identities passed. Reporter RNA/plasmid activity is normalized to the median 4×blank (BBBB) control.
Curation notes
The Methods identify N2A as ATCC CCL-131; Cellosaurus resolves Neuro-2a as CVCL:0470. The source workbook label is N2A. Counts are from Supplementary Data 6; the processed table uses the shared Supplementary Data 2 plasmid-input counts.