Experiment / E8TBPISQCSingle-Cell MPRA (scMPRA / sc-lentiMPRA)

Gnb3 promoter variant single-cell MPRA in ex vivo mouse retina

A single-cell massively parallel reporter assay detects cell-type-specific gene regulation

A 115-member library containing two independently synthesized wild-type Gnb3 promoter controls and 113 targeted promoter variants was introduced into newborn mouse retinas by electroporation and measured by scMPRA in Rod, Bipolar, Glia, and Neuron cells. The table joins full promoter sequences to author mean activities across two biological replicates and derives effects relative to the two-copy wild-type reference in each cell type.

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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: Mouse
Taxonomy ID: NCBITaxon:10090
Biosample: UBERON:0000966
Reference genome: Not reported / not applicable
Design focus: Variant-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated

Ex vivo P0 mouse-retina electroporation of a full-length Gnb3 promoter variant library driving mEmerald, with a constitutive U6 promoter expressing a second cBC copy to identify cells in which a promoter was sampled but silent. Gnb3 reporter barcodes, U6 barcodes, and 10x cell barcodes were linked to resolve promoter activity by retinal cell type.

Processed data

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Visible columns (33 of 33)

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Column dictionary · 33 definitions

element_id: Author variant name from Supplementary Table 5.
sequence: Full-length Gnb3 promoter variant sequence from Supplementary Table 5, normalized to uppercase.
sequence_length: Length of the Gnb3 promoter variant sequence in nucleotides.
order_name: Author ordering identifier for the Gnb3 variant oligo.
promoter_barcode: 8-bp promoter barcode (pBC) linked to the variant in Supplementary Table 5/6.
variant_class: Derived mutation family from the author variant name.
reference_variant_ids: Wild-type copies used as the within-cell-type reference (wt_1 and wt_2).
hamming_distance_to_wt1: Number of nucleotide differences from the wt_1 promoter sequence.
sequence_identity_to_wt1: Fraction of positions identical to wt_1.
rod_activity_rep1: Author Supplementary Table 6 mean activity in Rod cells, biological replicate 1.
rod_activity_rep2: Author Supplementary Table 6 mean activity in Rod cells, biological replicate 2.
rod_activity_mean: Arithmetic mean of the two author-reported Rod replicate activities.
rod_wt_reference_mean: Mean of wt_1 and wt_2 across both replicates in Rod; reference for relative effects.
rod_relative_to_wt: Rod activity mean divided by the two-copy WT reference mean.
rod_log2_fc_vs_wt: Log2 of the Rod activity mean divided by the two-copy WT reference mean; blank when activity mean is zero.
bipolar_activity_rep1: Author Supplementary Table 6 mean activity in Bipolar cells, biological replicate 1.
bipolar_activity_rep2: Author Supplementary Table 6 mean activity in Bipolar cells, biological replicate 2.
bipolar_activity_mean: Arithmetic mean of the two author-reported Bipolar replicate activities.
bipolar_wt_reference_mean: Mean of wt_1 and wt_2 across both replicates in Bipolar; reference for relative effects.
bipolar_relative_to_wt: Bipolar activity mean divided by the two-copy WT reference mean.
bipolar_log2_fc_vs_wt: Log2 of the Bipolar activity mean divided by the two-copy WT reference mean; blank when activity mean is zero.
glia_activity_rep1: Author Supplementary Table 6 mean activity in Glia cells, biological replicate 1.
glia_activity_rep2: Author Supplementary Table 6 mean activity in Glia cells, biological replicate 2.
glia_activity_mean: Arithmetic mean of the two author-reported Glia replicate activities.
glia_wt_reference_mean: Mean of wt_1 and wt_2 across both replicates in Glia; reference for relative effects.
glia_relative_to_wt: Glia activity mean divided by the two-copy WT reference mean.
glia_log2_fc_vs_wt: Log2 of the Glia activity mean divided by the two-copy WT reference mean; blank when activity mean is zero.
neuron_activity_rep1: Author Supplementary Table 6 mean activity in Neuron cells, biological replicate 1.
neuron_activity_rep2: Author Supplementary Table 6 mean activity in Neuron cells, biological replicate 2.
neuron_activity_mean: Arithmetic mean of the two author-reported Neuron replicate activities.
neuron_wt_reference_mean: Mean of wt_1 and wt_2 across both replicates in Neuron; reference for relative effects.
neuron_relative_to_wt: Neuron activity mean divided by the two-copy WT reference mean.
neuron_log2_fc_vs_wt: Log2 of the Neuron activity mean divided by the two-copy WT reference mean; blank when activity mean is zero.

Quality control

Author QC required correct-length cBC/rBC barcodes, corrected 10x barcodes by Hamming distance ≤1, retained high-confidence quads using the 1-read elbow threshold with Hamming rescue, and for retina removed unique barcode pairs containing only one UMI for a cBC. U6-based padding accounted for cells with a sampled but silent Gnb3 promoter. Supplementary Table 6 reports finite two-replicate activities for all 115 variants in all four retinal cell types; the package retains all 115. Relative-to-WT values are calculated from the mean of wt_1 and wt_2 across both replicates.

Curation notes

The retina is ex vivo tissue from newborn CD-1 IGS mice; UBERON:0000966 is used for retina. Variant names and sequence designs are preserved from Supplementary Table 5. Sequence differences are Hamming distances to wt_1; wt_2 is sequence-identical but has a different barcode. For zero author activity means, log2_fc_vs_wt is blank while the relative-to-WT ratio remains zero. No genomic assembly or exact Gnb3 promoter coordinates were stated in the accessible paper/data, so reference_genome and region_of_interest are null.

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