Experiment / E5QMB7Z6VEpisomal Plasmid MPRA

Eomes+ (IPC) in vivo immunoMPRA

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

The in vivo MPRA pool was delivered by in utero electroporation at E13.5, and fixed electroporated cells were immunostained for Eomes and isolated by FACS at E15.5 to enrich intermediate progenitor cells. DNA/RNA barcode counts are provided for two biological replicates over the shared enhancer and motif-mutant library.

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Organism: Mouse
Taxonomy ID: NCBITaxon:10090
Biosample: CL:0011020
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 Eomes, FACS-isolated, and then processed for paired DNA/RNA barcode counting.

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 Eomes+ archive contained 16,901 element rows; 9,712 passed these filters.

Curation notes

Eomes+ is the paper's IPC-enriched immunoFACS fraction. Cell Ontology has no exact intermediate-progenitor-cell class in the selected release, so the generic neural progenitor cell term CL:0011020 is used and the specific Eomes+/IPC label is retained in the experiment title and description. The archive is the GEO MPRA_EOMES file linked to GSM5583724/GSM5583725. 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 0.2391.

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