Experiment / E1L7TAR08Integrated lentiMPRA

Integrated lentiMPRA of candidate neuronal enhancers in human iPSC-derived neurons

Large-scale discovery of neural enhancers for cis-regulation therapies

A lentivirus-integrated MPRA tested 44,312 270-bp tiles covering 5,425 candidate neuronal cCREs, together with published active/inactive and scrambled controls, in WTC11-derived glutamatergic neurons. Three biological replicates were quantified by DNA/RNA barcode sequencing and DESeq2.

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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: Human
Taxonomy ID: NCBITaxon:9606
Biosample: CL:0000679
Reference genome: GRCh38
Design focus: Region-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated

Lentiviral integration of a 46,340-design reporter library (44,312 270-bp cCRE tiles with 90-bp overlaps, 100/99 NPC controls, 729/600 HAR controls, and 500 shuffled controls) into human WTC11/GM25256-derived glutamatergic neurons. Each design was associated with multiple 15-bp transcribed barcodes; three biological replicates were sequenced for DNA input and RNA output. Published analysis used MPRAflow/MPRAsnakeflow and DESeq2 with sequencing batch as a covariate; the processed table keeps the author's aggregate replicate counts, log2 RNA/DNA ratios, DESeq2 statistics, activity label, sequences, coordinates, and predicted target genes.

Processed data

50 rows per page. Click a cell to inspect its full value.

Visible columns (38 of 38)

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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 · 38 definitions

oligo_id: Unique published MPRA oligo/design identifier.
sequence: 270-bp test sequence as published, with original letter case preserved.
sequence_length_bp: Length of the published test sequence in base pairs.
sequence_class: Library class: Test, HAR_Positive, HAR_Negative, Inoue_Positive, Inoue_Negative, or Scrambled.
oligo_coordinates_hg38: Published GRCh38 interval for the 270-bp tested tile; blank for scrambled controls.
oligo_chrom: Chromosome parsed from the published tile interval.
oligo_start_hg38: Start coordinate parsed from the published tile interval.
oligo_end_hg38: End coordinate parsed from the published tile interval.
ccre_coordinates_hg38: Published candidate cis-regulatory element interval associated with the tile; blank for controls without a cCRE interval.
ccre_chrom: Chromosome parsed from the published cCRE interval.
ccre_start_hg38: Start coordinate parsed from the published cCRE interval.
ccre_end_hg38: End coordinate parsed from the published cCRE interval.
prediction_sources: Semicolon-separated enhancer prediction datasets whose source indicator equals 1 for the oligo.
predicted_target_genes: Merged predicted target-gene list supplied by the authors.
gw18_pfc_abc_genes: Target-gene list attributed to the GW18 PFC ABC prediction source.
ngn2_ipsc_abc_genes: Target-gene list attributed to the NGN2 iPSC ABC prediction source.
midfetal_cortex_ziffra_abc_genes: Target-gene list attributed to the midfetal cortex Ziffra ABC prediction source.
fetal_cerebrum_cicero_genes: Target-gene list attributed to the fetal cerebrum Cicero prediction source.
midfetal_cortex_trevino_genes: Target-gene list attributed to the midfetal cortex Trevino prediction source.
dna_rep1_count: Summed DNA barcode count for biological replicate 1 across sequencing batches.
dna_rep2_count: Summed DNA barcode count for biological replicate 2 across sequencing batches.
dna_rep3_count: Summed DNA barcode count for biological replicate 3 across sequencing batches.
rna_rep1_count: Summed RNA barcode count for biological replicate 1 across sequencing batches.
rna_rep2_count: Summed RNA barcode count for biological replicate 2 across sequencing batches.
rna_rep3_count: Summed RNA barcode count for biological replicate 3 across sequencing batches.
dna_mean_count: Published mean of the three biological-replicate DNA totals.
rna_mean_count: Published mean of the three biological-replicate RNA totals.
total_dna_count: Sum of the three DNA biological-replicate totals, calculated for this package.
total_rna_count: Sum of the three RNA biological-replicate totals, calculated for this package.
rep1_log2_count_ratio: Published log2 RNA/DNA count ratio for biological replicate 1.
rep2_log2_count_ratio: Published log2 RNA/DNA count ratio for biological replicate 2.
rep3_log2_count_ratio: Published log2 RNA/DNA count ratio for biological replicate 3.
mean_log2_count_ratio: Published mean of the three biological-replicate log2 RNA/DNA count ratios.
deseq2_log2_fold_change: Published DESeq2 RNA-versus-DNA log2 fold change.
deseq2_p_value: Published DESeq2 p-value for the RNA-versus-DNA contrast.
deseq2_fdr: Published Benjamini-Hochberg adjusted p-value for the DESeq2 contrast.
mpra_active: Published Is_Active MPRA activity call (TRUE or FALSE).
qc_pass: Package QC flag; TRUE for every row retained in table.csv.

Quality control

The authors combined two sequencing batches, summed DNA/RNA barcode counts across batches for three biological replicates, and tested RNA versus DNA with DESeq2 including batch as a covariate. Their code excluded library elements with total DNA barcode count <5; the package therefore retains only rows with non-missing DESeq2 log2 fold-change, p-value, FDR, and Is_Active fields (44,195 of 46,346 downloaded Supplementary Table S3 rows; 9,547 published active and 34,648 inactive). All retained rows have 270-bp sequences and unique oligo IDs. The 2,151 rows without sufficient DNA counts/statistics were excluded.

Curation notes

The processed table is built from the authors' Supplementary Table S3 (media-3_MPRA_library_and_results.csv), the primary source for the published counts and statistics. IGVF files in raw_data preserve released design, barcode, aggregate, and effect data for provenance but were not mixed into processed values because released IGVF aggregate RNA counts differ from the Supplementary Table S3 batch-summed RNA totals for many elements, consistent with a distinct processing/release version. The manuscript prose says active oligos require log2FoldChange >1 and FDR <0.01, but the published Is_Active column and repository R code yield 9,547 active rows using log2FoldChange >0 and FDR <0.01; this package preserves the published Is_Active label and exposes the DESeq2 values so users can apply either cutoff. Scrambled controls lack genomic coordinates by design. The downloaded Supplementary Table S3 contains six duplicate raw rows; these are among the rows excluded by the stated QC filter.

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