A 145-bp variant-focused oligonucleotide library representing major/reference and minor/alternate alleles across three variant-centered sliding windows was transfected into K562 cells overexpressing GATA1. Reporter RNA was measured 48 hours after transfection and normalized to plasmid DNA input across four GATA1-condition RNA replicates.
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:0004
Reference genome
hg19
Design focus
Variant-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
GATA1 overexpression
The pMPRA1/minP-luc2 episomal reporter library contained approximately 145-bp genomic inserts centered on each tested variant, with reference and alternate alleles placed in left, middle, and right sliding windows. Each construct was assigned 14 designed 11-nt barcodes. The pooled plasmid library was introduced into K562 cells overexpressing GATA1 by nucleofection; plasmid DNA input was sequenced in two replicates and reporter RNA output was sequenced after 48 hours in four K562+GATA1 replicates.
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 · 36 definitions
construct_id
Exact GEO construct name, including allele, sliding-window geometry, and source class.
variant_id
Stable package variant key in the form chr:position:reference>alternate; the GEO source did not provide dbSNP rs identifiers.
chromosome
hg19 chromosome without a chr prefix.
position_hg19
1-based hg19 coordinate of the tested variant.
ref_allele
Reference allele reported in the GEO raw matrix.
alt_allele
Alternate allele reported in the GEO raw matrix.
allele_label
GEO construct allele label: Ref or Mut.
allele
Normalized allele label: reference for Ref, alternate for Mut.
clean_class
GEO source construct class: var or mod.
window
Variant-centered sliding-window label: left, middle, or right.
window_geometry
Fraction of the 145-bp insert on the 5-prime and 3-prime sides of the variant.
sequence_145bp
145-bp genomic insert sequence for this allele and window.
n_barcodes_total
Number of designed barcodes for the construct; the source design assigns 14.
n_barcodes_qc
Number of barcodes with at least one DNA and one K562+GATA1 RNA replicate meeting the raw-count >=8 eligibility threshold.
n_dna_observations_qc
Number of DNA barcode-replicate observations contributing to the normalized activity summary after the count threshold.
n_rna_observations_qc
Number of K562+GATA1 RNA barcode-replicate observations contributing to the normalized activity summary after the count threshold.
dna_rep1_barcodes_count_ge_8
Number of the 14 barcode rows with K562_minP_DNA1 raw count >=8.
dna_rep2_barcodes_count_ge_8
Number of the 14 barcode rows with K562_minP_DNA2 raw count >=8.
dna_rep1_count_sum
Raw K562_minP_DNA1 counts summed over all 14 source barcode rows.
dna_rep2_count_sum
Raw K562_minP_DNA2 counts summed over all 14 source barcode rows.
rna_rep1_count_sum
Raw K562_GATA1_minP_RNA1 counts summed over all 14 source barcode rows.
rna_rep1_barcodes_count_ge_8
Number of the 14 barcode rows with K562_GATA1_minP_RNA1 raw count >=8.
rna_rep2_count_sum
Raw K562_GATA1_minP_RNA2 counts summed over all 14 source barcode rows.
rna_rep2_barcodes_count_ge_8
Number of the 14 barcode rows with K562_GATA1_minP_RNA2 raw count >=8.
rna_rep3_count_sum
Raw K562_GATA1_minP_RNA3 counts summed over all 14 source barcode rows.
rna_rep3_barcodes_count_ge_8
Number of the 14 barcode rows with K562_GATA1_minP_RNA3 raw count >=8.
rna_rep4_count_sum
Raw K562_GATA1_minP_RNA4 counts summed over all 14 source barcode rows.
rna_rep4_barcodes_count_ge_8
Number of the 14 barcode rows with K562_GATA1_minP_RNA4 raw count >=8.
dna_mean_log2_cpm
Mean pseudocount-adjusted log2 DNA CPM across eligible barcode-level DNA observations.
rna_mean_log2_cpm
Mean pseudocount-adjusted log2 K562+GATA1 RNA CPM across eligible barcode-level RNA observations.
log2_rna_dna_activity
Construct activity, calculated as rna_mean_log2_cpm minus dna_mean_log2_cpm.
activity_sd_across_barcodes
Sample standard deviation of eligible barcode-level log2 RNA/DNA activities.
activity_se_across_barcodes
Standard error of the eligible barcode-level log2 RNA/DNA activity mean.
allelic_log2_fc_alt_minus_ref
Package-derived alternate-construct activity minus reference-construct activity for the same variant, window, and source class; blank if the paired construct did not pass QC.
allelic_pair_qc
TRUE when both reference and alternate constructs in the same variant/window/source-class pair passed QC.
qc_pass
TRUE for every construct retained in this processed table after the package QC filter.
Quality control
The authors added a pseudocount of 1, normalized DNA and RNA barcode counts to counts per million (CPM), log2-transformed the values, removed barcode observations below the reported count threshold of 8 per replicate, and assessed allelic effects with two-sided Mann-Whitney U tests using FDR <1%. For this package, a barcode was eligible for this condition when at least one of the two DNA replicates and at least one of the four K562+GATA1 RNA replicates had a raw count >=8; a construct was retained only when at least 5 of its 14 barcodes were eligible. The table contains 14,878 retained constructs from the 16,534 GEO source constructs; all rows have qc_pass=TRUE. Construct activity is the mean barcode-level log2 RNA/DNA score across eligible barcodes, and the paired alternate-minus-reference effect is populated only when both allele constructs pass QC.
Curation notes
The GEO matrix is a processed barcode-count source rather than raw FASTQ. The design and barcode-mapping files are retained in raw_data and validate the 14-barcode construct layout. Source coordinates are hg19 and the source matrix does not include rs identifiers, so variant_id preserves the coordinate and allele identity. Source-marked mod constructs are retained because they are part of the published library. Shared plasmid-DNA replicates are used for both condition-specific experiments. The package-derived activity and paired allelic effect are intended as clean research summaries and are not claimed to reproduce the paper's fitted FDR statistics exactly.