Experiment / E67OBEP6ZEpisomal Plasmid MPRA

Bulk in vivo MPRA of electroporated E15.5 cortex

Multimodal profiling of the transcriptional regulatory landscape of the developing mouse cortex identifies Neurog2 as a key epigenome remodeler

An in vivo episomal MPRA pool was delivered by in utero electroporation at E13.5 and recovered 48 h later from mScarlet-I-positive E15.5 somatosensory cortex cells. The library contains wild-type enhancer classes, scrambled controls, and transcription-factor motif-mutant constructs, with DNA/RNA barcode counts from two biological replicates.

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Organism: Mouse
Taxonomy ID: NCBITaxon:10090
Biosample: UBERON:0008933
Reference genome: mm10
Design focus: Region-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated

In vivo plasmid MPRA using pMPRA1-derived constructs. 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 link constructs to reporter RNA and plasmid DNA. The pool was introduced by IUE into E13.5 cortex, and mScarlet-I-positive cells were FACS-isolated at E15.5; RNA and DNA were quantified by MPRAflow.

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 · 28 definitions

element_id: Construct/CRE identifier from the GEO count matrix.
sequence: 270-bp supplied design sequence: the 266-bp CRE plus its 4-bp construct identifier tag.
sequence_length: Length of the supplied design sequence in base pairs.
sequence_class: Paper/GEO library annotation, such as WTposCor, WTnegCor, WTnoCor, scrContr, or a motif-mutant class.
element_category: Package-derived broad category: wild_type_enhancer, named_enhancer, scrambled_control, or motif_mutant.
library_barcode_count: Number of filtered CRE-associated 12-bp barcodes in the plasmid barcode-association pickle.
source_chrom: Chromosome parsed from the construct identifier's original source-region coordinates; blank for scrambled controls.
source_start: Start of the original 500-bp source region encoded in the construct identifier.
source_end: End of the original 500-bp source region encoded in the construct identifier.
source_region_length: End minus start for the original source region; the supplied construct IDs encode 500-bp regions.
dna_count_rep1: Sum of DNA barcode counts in replicate 1 after dropping barcode positions with zero RNA.
rna_count_rep1: Sum of RNA barcode counts in replicate 1 after dropping barcode positions with zero DNA.
dna_barcodes_rep1: Number of barcode positions with at least one DNA read in replicate 1, before the paired-DNA/RNA filter.
rna_barcodes_rep1: Number of barcode positions with at least one RNA read in replicate 1, before the paired-DNA/RNA filter.
shared_barcodes_rep1: Number of barcode positions with at least one read in both DNA and RNA in replicate 1.
dna_count_rep2: Sum of DNA barcode counts in replicate 2 after dropping barcode positions with zero RNA.
rna_count_rep2: Sum of RNA barcode counts in replicate 2 after dropping barcode positions with zero DNA.
dna_barcodes_rep2: Number of barcode positions with at least one DNA read in replicate 2, before the paired-DNA/RNA filter.
rna_barcodes_rep2: Number of barcode positions with at least one RNA read in replicate 2, before the paired-DNA/RNA filter.
shared_barcodes_rep2: Number of barcode positions with at least one read in both DNA and RNA in replicate 2.
dna_cpm_rep1: Paired-filtered DNA count normalized to the total paired-filtered DNA library count as counts per million in replicate 1.
rna_cpm_rep1: Paired-filtered RNA count normalized to the total paired-filtered RNA library count as counts per million in replicate 1.
log2_activity_rep1: Package-derived log2((RNA CPM + 1) / (DNA CPM + 1)) activity score for replicate 1.
dna_cpm_rep2: Paired-filtered DNA count normalized to the total paired-filtered DNA library count as counts per million in replicate 2.
rna_cpm_rep2: Paired-filtered RNA count normalized to the total paired-filtered RNA library count as counts per million in replicate 2.
log2_activity_rep2: Package-derived log2((RNA CPM + 1) / (DNA CPM + 1)) activity score for replicate 2.
mean_log2_activity: Arithmetic mean of the two replicate log2 activity scores.
replicate_delta_log2_activity: Replicate 2 log2 activity minus replicate 1 log2 activity.

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 bulk archive contained 17,236 element rows; 12,782 passed these filters.

Curation notes

This is the heterogeneous mScarlet-I-positive bulk fraction, not an immunoFACS-defined cell type. The archive is the GEO MPRA_pool file linked to GSM5583720/GSM5583721. The compact GEO archive does not include the paper's MPRAnalyze alpha.score table, so log2_activity_* is a transparent CPM-normalized RNA/DNA score calculated here from the deposited MPRAflow counts; it should not be interpreted as the paper's mad.score. The Pearson correlation of the package-derived element activity between replicates is 0.3711.

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