The same 461-element MPRAi plasmid library, with 20 designed barcodes per element, was transfected into five HMC3 human microglial replicates. DNA and RNA barcode counts quantify plasmid representation and reporter activity in the in vitro cell-line arm.
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
CVCL:II76
Reference genome
Not reported / not applicable
Design focus
Region-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Basal / Untreated
HMC3 cells were transfected with the pAAV-Hsp68-nls/mCherry-MPRAi plasmid library; construct output was read from barcode amplicon counts in RNA relative to plasmid DNA. After paper-reported modality-specific QC, the table contains RNA-only HMC3 A/B/E and DNA-only HMC3 C/D measurements; no retained HMC3 sample has both modalities, so the derived RNA/DNA ratio is blank.
Processed data
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Visible columns (37 of 37)
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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 · 37 definitions
element_id
Unique enhancer, variant, or control construct identifier from Supplementary Table S2.
sequence
120-bp tested enhancer or control sequence.
sequence_length
Length of the tested sequence in nucleotides.
barcode_design_count
Number of designed barcodes for the element in the library; 20 for every element.
barcode_count_table_rows
Number of observed barcodes assigned to the element in the supplied DNA/RNA count matrices.
library_dna_detected_barcodes
Number of the element's designed barcodes marked dnaDetect=TRUE in Supplementary Table S2.
library_rna_detected_barcodes
Number of the element's designed barcodes marked rnaDetect=TRUE in Supplementary Table S2.
source
Top-level source label for the library construct.
sub_source
Detailed library design/control category from Supplementary Table S2.
design_group
Human-readable interpretation of the library design category.
control_status
Whether the construct is a positive control, negative control, candidate enhancer, or variant construct.
variant_family
Shared family identifier for linked allele or MEF2C constructs; blank for non-variant designs.
variant_state
State of a linked construct, such as reference, alternate, motif-disrupted, or shuffled.
paired_element_id
Element identifier(s) linked for direct allele or MEF2C construct comparison.
sample_id
Sample/run identifier from Supplementary Table S3.
tissue
Tissue or cell type reported for the sample.
replicate_or_animal
Cell replicate label reported for the sample.
nova_run
NovaSeq run number reported for the sample.
sample_rna_quality
Paper-reported RNA sample QC tier, blank when RNA was unavailable for the retained measurement.
sample_dna_quality
Paper-reported DNA sample QC tier, blank when DNA was unavailable for the retained measurement.
paper_qc_pass
TRUE for rows retained after the paper-reported sample/modality QC; failing entries are omitted.
measurement_type
Available retained modalities: paired_DNA_RNA, RNA_only, or DNA_only.
sample_total_dna_counts
Total DNA barcode counts across all observed barcode rows in the source matrix for this sample.
sample_total_rna_counts
Total RNA barcode counts across all observed barcode rows in the source matrix for this sample.
dna_count
Sum of raw DNA barcode counts for this element across its observed barcodes.
rna_count
Sum of raw RNA barcode counts for this element across its observed barcodes.
dna_cpm
Element DNA count per million total DNA barcode counts in the source sample.
rna_cpm
Element RNA count per million total RNA barcode counts in the source sample.
dna_barcodes_with_reads
Number of observed element barcodes with DNA count greater than zero.
rna_barcodes_with_reads
Number of observed element barcodes with RNA count greater than zero.
log2_rna_dna_ratio
Derived log2 of library-size-normalized RNA/DNA counts using a +1 count pseudocount; blank because no retained HMC3 sample has both modalities.
published_test_type
Published supplementary statistical test associated with the element or construct family, when available.
published_baseline_alpha
Baseline alpha value from the published MEF2C family-level test.
published_baseline_mad
Baseline median absolute deviation value from the published MEF2C family-level test.
published_test_statistic
Test statistic from Supplementary Table S7 or S8.
published_test_pvalue
P-value from Supplementary Table S7 or S8.
published_test_significant
TRUE/FALSE significance flag from S8 or derived as p<0.05 for S7.
Quality control
Applied the authors' HMC3 QC decisions: HMC3 C RNA was excluded for low experimentally measured RNA quality and low correlation with the other HMC3 RNA samples, while HMC3 E DNA was excluded for poor DNA correlation (R=0.81 versus median R=0.95). The passing modalities were retained as RNA-only or DNA-only rows rather than being discarded with the failing modality. All 461 elements had at least one mapped observed barcode.
Curation notes
Long-form table has 2,305 rows: 461 elements across five HMC3 replicates. The paper's modality-specific exclusions mean HMC3 A/B/E contribute RNA-only rows and HMC3 C/D contribute DNA-only rows; no HMC3 log2 RNA/DNA values are invented. The final library annotation contains 461 elements and 9,220 designed barcode records; the supplied Supplementary Tables S4/S5 used for aggregation contain 3,983 observed barcode rows, while the retained GEO mirrors contain all 9,220 designed barcode rows including zero/low-count rows. Published MEF2C and AD-associated variant test values are retained where they map to the construct or family. HMC3 is identified by Cellosaurus CVCL:II76.