Two replicate episomal MPRAs in the same H9-derived human neural stem cell system tested validation fragments and synthetic combinations of human-specific and ancestral alleles on human and chimpanzee background sequences. The library also included negative controls, positive controls, and tile/other control fragments.
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:0000047
Reference genome
GRCh37/hg19
Design focus
Variant-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Basal / Untreated
The second library included identical validation copies of active fragments and artificial fragments containing all possible combinations of hSub states on human or chimpanzee background sequences, plus negative and positive controls. H and C in allele_state denote human and chimpanzee/ancestral sequence states rather than nucleotide letters. Two hNSC replicate libraries were measured by input pDNA and reporter cDNA barcode sequencing; the table preserves the GEO Type, Subtype, Species, Allele, BG, maxID, and Pos design annotations and adds fragment-level median barcode activity.
Processed data
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Visible columns (35 of 35)
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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 · 35 definitions
fragment_id
GEO Alignment identifier for the tested synthetic fragment.
position_group
GEO Pos interval identifying the locus/fragment group shared by related allele-state constructs.
sequence_type
GEO Type classification, including hsSUB, tile, and control classes.
sequence_subtype
GEO Subtype classification, including Add, NonAdd, tile, and control subtype labels.
sequence_background
GEO BG background indicator, with B and NB denoting the supplied construct backgrounds.
tested_sequence_species
GEO Species field describing the human or chimpanzee sequence/background label.
allele_state
GEO H/C/X state string for the tested construct; H and C represent human and chimpanzee/ancestral states and X is used for non-allelic controls.
allele_state_count
Number of H/C state characters in allele_state.
reference_role
Derived role: human_reference, chimp_reference, synthetic_or_variant_state, control, or tile_or_other.
source_n_field
Original GEO n field retained without reinterpretation.
max_id
Original GEO maxID value for the fragment.
human_hg19_chrom
Human GRCh37/hg19 chromosome parsed from the Pos interval.
human_hg19_start
Human GRCh37/hg19 fragment start parsed from the Pos interval.
human_hg19_stop
Human GRCh37/hg19 fragment stop parsed from the Pos interval.
hsub_count_in_interval
Number of author-mapped hSub positions falling inside the Pos interval.
hsub_hg19_positions
Author-mapped GRCh37/hg19 hSub positions inside the Pos interval.
region_class
Derived broad class of mapped annotation: HGE, HAR, or HACNS.
region_labels
Author-provided enhancer/HAR labels overlapping hSub positions in the interval.
phyloP_scores
Author-provided GRCh37/hg19 phyloP scores at hSub positions in the interval.
tad_genes
Genes listed by the authors as occurring in TADs associated with hSub positions in the interval.
tfbs_factors
Expressed transcription factors from author-provided hSub/TFBS intersections in the interval.
source_barcode_count
Number of barcode rows for the fragment before low-count QC.
qc_barcode_count
Number of barcode rows retained after the published low-count QC filter.
retained_barcode_fraction
qc_barcode_count divided by source_barcode_count.
pdna_rep1_count_sum
Sum of input pDNA counts for replicate 1 across retained barcode rows.
pdna_rep2_count_sum
Sum of input pDNA counts for replicate 2 across retained barcode rows.
cdna_rep1_count_sum
Sum of reporter cDNA counts for replicate 1 across retained barcode rows.
cdna_rep2_count_sum
Sum of reporter cDNA counts for replicate 2 across retained barcode rows.
activity_rep1_log2
Median barcode-level log2(cDNA/pDNA) activity for replicate 1 after library-size normalization.
activity_rep2_log2
Median barcode-level log2(cDNA/pDNA) activity for replicate 2 after library-size normalization.
mean_activity_log2
Mean of the two replicate-level median log2 activities.
median_activity_log2
Median of the two replicate-level median log2 activities.
sd_activity_across_replicates
Standard deviation of the two replicate-level median log2 activities.
reference_human_minus_chimp_mean_log2_activity
Mean activity of the human reference state minus the chimpanzee reference state within a position_group, when both were measured and passed QC.
qc_pass
TRUE for rows retained after barcode and fragment-depth QC.
Quality control
Following the authors' RD2 analysis logic, pDNA and cDNA count columns were library-size normalized and log2 transformed after adding a 0.1 pseudocount. Barcode rows with mean normalized pDNA count below -5.25 across the two pDNA replicates were excluded. Fragments were retained only when at least 12 barcodes remained, yielding 22,764 measured fragments. Experimental and control fragments were retained together; no additional activity-direction filter was applied to the table. Reference roles and human-minus-chimpanzee contrasts were derived from the raw H/C allele-state and background fields.
Curation notes
The table contains one row per measured MPRA2 construct. reference_role is an explicit derivation from the source H/C allele_state, Species, Type, and BG fields; the reference contrast is populated only for position groups containing both human_reference and chimp_reference constructs. The H/C strings do not provide actual nucleotide identities, so nucleotide-level hSub changes are intentionally not inferred. The biosample is an in-vitro H9-derived neural stem cell population, mapped to CL:0000047 (neuronal stem cell; neural stem cell synonym).