Cell-type-specific episomal MPRA in human cortical organoid PAX6-negative/EOMES-negative (N) cells
Joint epigenome profiling reveals cell-type-specific gene regulatory programmes in human cortical organoidsA common 5,876-sequence episomal MPRA library was electroporated into day-45 human cortical organoids, cultured for 72 hours, and assayed after immunoFACS isolation of the PAX6-negative/EOMES-negative N population in two biological replicates. The table combines the published per-construct N activity statistics with normalized DNA/RNA barcode summaries calculated from the GEO processed count matrix.
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.
Perturbation & assay details
Basal / Untreated
The library contained 2,737 differentially accessible regions linked to differentially expressed genes, 267 MER130/UCON31 transposable-element sequences, 2,372 motif-mutated enhancer sequences, and 500 scrambled controls. Inserts were 266-bp hg38 sequences with a 4-bp wild-type/control or mutant tag and 12-bp barcodes in a pMPRA1 mScarlet-I minimal-promoter reporter. The fixed, immunoFACS-sorted PAX6-negative/EOMES-negative DNA and RNA libraries were processed with MPRAflow. Package-derived ratio-of-sums metrics follow the paper's replicate-comparison code after retaining barcodes with nonzero counts in both DNA and RNA.
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 · 33 definitions
- sequence_id
- Unique tested construct identifier from Supplementary Table 5.
- element_type
- Authors' enh_typ class (WT, scr, or motif/element-specific mutant label).
- construct_class
- Authors' class (WT, mut, or scr).
- source_enhancer_class
- Authors' enh_class annotation (RGC, IPC, or blank when #N/A).
- chromosome
- Chromosome parsed from the source coordinate when present.
- center_position_hg38
- Source center coordinate on GRCh38/hg38; blank for scrambled/TE identifiers without coordinates.
- center_coordinate_hg38
- Source coordinate in chr:start form.
- linked_gene
- Linked gene label from Supplementary Table 5.
- vista_enhancer
- VISTA enhancer identifier from Supplementary Table 5.
- dna_read_sum_rep1
- Library-size-normalized DNA count sum for replicate 1 after paired DNA/RNA barcode filtering; package-derived.
- rna_read_sum_rep1
- Library-size-normalized RNA/cDNA count sum for replicate 1 after paired DNA/RNA barcode filtering; package-derived.
- dna_barcodes_rep1
- Number of nonzero paired DNA barcodes in replicate 1 after the paired-count filter.
- rna_barcodes_rep1
- Number of nonzero paired RNA barcodes in replicate 1; the same paired barcode set is used.
- dna_read_sum_rep2
- Library-size-normalized DNA count sum for replicate 2 after paired DNA/RNA barcode filtering; package-derived.
- rna_read_sum_rep2
- Library-size-normalized RNA/cDNA count sum for replicate 2 after paired DNA/RNA barcode filtering; package-derived.
- dna_barcodes_rep2
- Number of nonzero paired DNA barcodes in replicate 2 after the paired-count filter.
- rna_barcodes_rep2
- Number of nonzero paired RNA barcodes in replicate 2; the same paired barcode set is used.
- ratio_sums_rep1
- (normalized RNA read sum + 1)/(normalized DNA read sum + 1) for replicate 1.
- ratio_sums_rep2
- (normalized RNA read sum + 1)/(normalized DNA read sum + 1) for replicate 2.
- mean_ratio_sums
- Mean of the two replicate ratio_sums values.
- mean_log2_ratio_sums
- Mean of log2(ratio_sums) across the two replicates; package-derived log2 activity summary.
- raw_count_status
- Whether sequence_id occurs in the GEO compact processed count matrix.
- paired_barcode_status
- Whether paired DNA/RNA barcodes are available in both, one, or neither replicate; not_available when the raw row is absent.
- mpra_statistic
- Published N-specific MPRA statistic from Supplementary Table 5.
- mpra_mad_score
- Published N-specific MAD score (reporter activity signal).
- mpra_zscore
- Published N-specific z-score.
- mpra_empirical_p_value
- Published N-specific empirical p-value.
- mpra_mad_p_value
- Published N-specific MAD-based p-value; the source analysis uses <= 0.1 to call active enhancers.
- mpra_zscore_p_value
- Published N-specific z-score-based p-value.
- mpra_control
- Whether the source row is one of the 492 scrambled controls.
- published_active_fdr_le_0_1
- Boolean derived from mpra_mad_p_value <= 0.1.
- qc_status
- Package QC status; PASS_PUBLISHED_MPRA_QC rows have finite statistic, MAD score, and MAD p-value in [0,1].
- source_table
- Source workbook sheet used for published metrics.
Quality control
The authors report recovery of more than 98% of the 5,876 library sequences. Supplementary Table 2 reports N replicate 1 DNA 9,512,315 total/9,098,841 mapped reads and RNA 24,225,140/21,908,634 mapped reads; replicate 2 DNA 19,868,211/18,771,185 and RNA 30,764,615/27,912,363. Reads were trimmed with cutadapt, barcode/CRE associations were generated by MPRAflow, and MPRAanalyse identified active enhancers using mad.score with Benjamini–Hochberg-adjusted p <= 0.1. The paper states that no data were excluded. Package QC retained all 5,661 Supplementary Table 5 rows because each had finite published statistic, MAD score, and MAD p-value in [0,1]; no rows were filtered. GEO processed count archives cover 4,942 of these rows; raw-derived columns are blank for published rows absent from the compact GEO matrix, with raw_count_status documenting coverage.
Curation notes
The paper calls this population PAX6−EOMES− (N); GEO labels its archive NEG and the analysis repository uses PN. It is a gate-defined population rather than an explicitly assigned pure terminal cell type, so the biosample is marked UNMAPPED rather than mapped to a broader neuron term. center_coordinate_hg38 is the source name coordinate, not an inferred interval. source_enhancer_class is the authors' Table 5 annotation. The processed table is condition-specific; cross-cell-type published scores are in the sibling experiments. Published result rows absent from the compact GEO matrix are retained with blank raw-derived fields, while the downloaded archive preserves the underlying available count data.