Four replicate episomal MPRAs in H9-derived human neural stem cells tested 137-bp human and chimpanzee orthologous fragments centered on human-specific substitutions in HARs and HGEs. Barcode counts from input plasmid DNA and reporter cDNA were summarized to quantify fragment enhancer activity and human-versus-chimpanzee differences.
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
Synthetic 137-bp fragments were cloned upstream of a minimal promoter driving a luc2 firefly luciferase reporter with a random oligonucleotide barcode. Human (hg19) and chimpanzee (PanTro2) orthologs were included in the same library; the study reported about 80 barcodes per fragment and four hNSC replicates. Input pDNA and total-RNA-derived cDNA barcode libraries were paired-end sequenced on Illumina HiSeq 4000 instruments. The table reports fragment-level medians of barcode log2(cDNA/pDNA) activity for each replicate, raw count sums, and human–chimpanzee paired contrasts.
Processed data
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Visible columns (44 of 44)
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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 · 44 definitions
fragment_id
GEO Alignment identifier for the tested fragment and species.
fragment_pair_id
Orthologous pair identifier formed by removing the trailing chimpanzee suffix; human and chimpanzee rows can be paired on this value.
fragment_design
Whether the alignment is an hSub-containing fragment or another fragment type.
tested_sequence_species
Species represented by the tested sequence: hg19 human or PanTro2 chimpanzee.
source_contig
Reference contig from the raw GEO row for the tested sequence.
source_start
Raw GEO start coordinate for the tested sequence.
source_stop
Raw GEO stop coordinate for the tested sequence.
human_hg19_chrom
Human GRCh37/hg19 chromosome encoded by the alignment identifier.
human_hg19_start
Human GRCh37/hg19 fragment start encoded by the alignment identifier.
human_hg19_stop
Human GRCh37/hg19 fragment stop encoded by the alignment identifier.
ortholog_sequence_id
Ortholog_Seq identifier supplied by GEO.
hsub_count
Number of human-specific substitution positions listed for the fragment.
hsub_changes
Per-position base changes supplied in the raw GEO annotation, in semicolon-separated order.
hsub_positions_in_fragment_0based
Zero-based positions of hSubs within the fragment, supplied by GEO.
hsub_hg19_positions
Absolute GRCh37/hg19 positions derived from the alignment start plus the zero-based fragment offsets.
region_class
Derived broad class of mapped annotation: HGE, HAR, or HACNS.
region_labels
Author-provided enhancer/HAR labels overlapping the hSub positions.
phyloP_scores
Author-provided GRCh37/hg19 phyloP scores at the hSub positions.
tad_genes
Genes listed by the authors as occurring in TADs associated with the hSub positions.
tfbs_factors
Expressed transcription factors from the author-provided hSub/TFBS intersections.
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.
inert_count_sum
Sum of inert-library counts across retained barcode rows.
competent_count_sum
Sum of competent-library counts across retained barcode rows.
cdna_rep1_count_sum
Sum of reporter cDNA counts for experimental replicate 1 across retained barcode rows.
cdna_rep2_count_sum
Sum of reporter cDNA counts for experimental replicate 2 across retained barcode rows.
cdna_rep3_count_sum
Sum of reporter cDNA counts for experimental replicate 3 across retained barcode rows.
cdna_rep4_count_sum
Sum of reporter cDNA counts for experimental replicate 4 across retained barcode rows.
pdna_rep1_count_sum
Sum of input pDNA counts for experimental replicate 1 across retained barcode rows.
pdna_rep2_count_sum
Sum of input pDNA counts for experimental replicate 2 across retained barcode rows.
pdna_rep3_count_sum
Sum of input pDNA counts for experimental replicate 3 across retained barcode rows.
pdna_rep4_count_sum
Sum of input pDNA counts for experimental replicate 4 across retained barcode rows.
activity_rep1_log2
Median barcode-level log2(cDNA/pDNA) activity for experimental replicate 1 after library-size normalization.
activity_rep2_log2
Median barcode-level log2(cDNA/pDNA) activity for experimental replicate 2 after library-size normalization.
activity_rep3_log2
Median barcode-level log2(cDNA/pDNA) activity for experimental replicate 3 after library-size normalization.
activity_rep4_log2
Median barcode-level log2(cDNA/pDNA) activity for experimental replicate 4 after library-size normalization.
mean_activity_log2
Mean of the four replicate-level median log2 activities.
median_activity_log2
Median of the four replicate-level median log2 activities.
sd_activity_across_replicates
Standard deviation of the four replicate-level median log2 activities.
human_minus_chimp_mean_log2_activity
Human hg19 mean activity minus PanTro2 chimpanzee mean activity for a paired fragment, when both rows passed QC.
author_permissive_active
Whether the exact fragment identifier occurs in the authors' permissive MWU active-fragment list.
author_permissive_differential
Whether the exact fragment identifier occurs in the authors' permissive MWU differential-activity list.
qc_pass
TRUE for rows retained after barcode and fragment-depth QC.
Quality control
Following the authors' RD1 analysis logic, each count column was library-size normalized and log2 transformed after adding a 0.1 pseudocount. Barcode rows with mean normalized count below -5.25 across the competent-library count and four experimental pDNA replicates were excluded. Fragments were retained only when at least 12 barcodes remained, yielding 78,487 measured fragments. No additional activity-direction filter was applied to the table; author-provided permissive active and differential-activity calls are retained as boolean annotations.
Curation notes
The table contains one row per species-specific measured fragment, not one row per orthologous pair; 68,228 rows have a paired human-minus-chimpanzee contrast because both species rows passed QC. The author-provided permissive call flags are carried over from MWU_active_fragments.lst and MWU_da_fragments.lst and were not recomputed here. Chimpanzee rows retain PanTro2 source coordinates while human_hg19_* fields identify the corresponding human alignment interval. The biosample is an in-vitro H9-derived neural stem cell population, mapped to CL:0000047 (neuronal stem cell; neural stem cell synonym).