Pax6+ (NSC) in vivo immunoMPRA

The in vivo MPRA pool was delivered by in utero electroporation at E13.5, and fixed electroporated cells were immunostained for Pax6 and isolated by FACS at E15.5 to enrich neural stem cells. DNA/RNA barcode counts are provided for two biological replicates over the shared enhancer and motif-mutant 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: CL:0000047
Reference genome: mm10
Design focus: Region-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated

In vivo immunoMPRA using episomal pMPRA1-derived constructs delivered by IUE. Each design is a 266-bp mm10 CRE with a 4-bp WT/control or mutant identifier tag in the supplied 270-bp FASTA sequence; degenerate 12-bp barcodes are read from reporter RNA and plasmid DNA. Fixed electroporated cells were immunostained for Pax6, FACS-isolated, and then processed for paired DNA/RNA barcode counting.

Quality control

The deposited count matrices were produced after cutadapt trimming and MPRAflow barcode counting; the paper used MPRAnalyze and defined significant activity with mad.score P <= 0.05. For this package, barcode positions with zero DNA or zero RNA were excluded from element-level sums, following the paired-DNA/RNA filter in the authors' analysis code. Elements were retained only when at least 3 paired barcode positions were present in each biological replicate, had a matching design sequence, and produced finite CPM-normalized activity scores. The Pax6+ archive contained 16,802 element rows; 8,614 passed these filters.

Curation notes

Pax6+ is the paper's NSC-enriched immunoFACS fraction. The archive is the GEO MPRA_PAX6 file linked to GSM5583722/GSM5583723. The compact GEO archive does not include the paper's MPRAnalyze mad.score table, so log2_activity_* is a transparent CPM-normalized RNA/DNA score calculated here from the deposited MPRAflow counts. The Pearson correlation of the package-derived element activity between replicates is 0.1522; this lower agreement is consistent with the sparser immunoMPRA barcode recovery and is reported as an assay-level caveat.

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Pax6+ (NSC) in vivo immunoMPRA

Processed data

Quality control

Curation notes

Cite OpenMPRA

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