The same RSV-promoter plasmid MPRA library included 114-bp enhancer oligonucleotides tiled at approximately 50-bp intervals across 14 autoimmune disease-associated loci and positive/negative control regions. This table reports primary-CD4-T-cell median quantile-normalized RNA/DNA activity in resting and stimulated states for every enhancer construct retained in the GEO processed file, with locus-level driver annotations from Appendix Table S1.
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.
Unstimulated/resting and four-day stimulation with 10 ng/ml IL-2 and anti-CD2/3/28 bead particles; RNA collected 24 h after nucleofection
Enhancer sequences were cloned into an episomal MPRA vector containing the RSV promoter and EGFP reporter, each tagged with six unique 11-nt barcodes. The library was transfected into primary CD4 T cells from 12 healthy donors in resting and stimulated states; construct-level RNA counts were normalized to the input plasmid DNA library. The table's RNA/DNA ratios and log2 activity values are derived from the GEO-supplied quantile-normalized, barcode-collapsed construct counts.
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 · 25 definitions
element_id
Unique barcode-library identifier for the enhancer construct.
construct_type
Library construct class; all rows in this table are Enhancer constructs.
coordinates_hg19
Inclusive genomic interval of the 114-bp enhancer oligonucleotide on hg19.
chromosome
Chromosome parsed from coordinates_hg19.
start_hg19
Inclusive hg19 start coordinate parsed from coordinates_hg19.
end_hg19
Inclusive hg19 end coordinate parsed from coordinates_hg19.
sequence_114bp
Synthesized enhancer sequence tested in the MPRA.
sequence_length_bp
Length in base pairs of sequence_114bp.
tiling_locus
Appendix Table S1 locus/control-region label containing the enhancer interval.
associated_disease
Disease association or control designation for the tiling locus from Appendix Table S1.
library_barcode_count
Number of barcode-library rows assigned to this construct in the GEO raw barcode file; the design used six barcodes per enhancer construct.
dna_median_quantile_normalized_count
Median of v1-v4 input plasmid DNA construct counts from the GEO quantile-normalized collapsed table.
resting_cd4_median_rna_quantile_normalized_count
Median of the 12 resting primary-CD4 RNA construct counts from the GEO quantile-normalized collapsed table.
resting_cd4_rna_over_dna
Resting primary-CD4 median RNA construct count divided by the median input DNA construct count.
resting_cd4_log2_rna_over_dna
Base-2 logarithm of resting_cd4_rna_over_dna; a derived construct activity score.
Median of the 12 stimulated primary-CD4 RNA construct counts from the GEO quantile-normalized collapsed table.
stimulated_cd4_rna_over_dna
Stimulated primary-CD4 median RNA construct count divided by the median input DNA construct count.
stimulated_cd4_log2_rna_over_dna
Base-2 logarithm of stimulated_cd4_rna_over_dna; a derived construct activity score.
n_cd4_resting_replicates
Number of resting primary-CD4 RNA replicates summarized (12).
n_cd4_stimulated_replicates
Number of stimulated primary-CD4 RNA replicates summarized (12).
driver_element_in_resting_cd4
Appendix Table S1 indicator that the locus contains a significant high-resolution driver element in resting CD4 T cells.
driver_element_in_stimulated_cd4
Appendix Table S1 indicator that the locus contains a significant high-resolution driver element in stimulated CD4 T cells.
driver_elements_bp_in_locus
Total base pairs identified as driver elements in either state for the locus, from Appendix Table S1.
qc_status
All rows are marked pass because they are present in the authors' post-QC GEO construct table.
source_dataset
Source of the normalized construct counts and locus-level tiling annotations.
Quality control
FastQC was applied to the sequencing data. A barcode was counted only when it exactly matched a library barcode and was followed by at least 10 bases of the expected constant sequence; successful transfection required at least 70% of the barcode library to be represented. Counts were CPM-normalized, barcodes with median CPM <0.5 in RNA or DNA were removed, identical constructs were summed, and construct counts were quantile-normalized. The processed table retains the 7,320 enhancer constructs present in the GEO normalized/collapsed file out of 7,690 unique enhancer constructs in the barcode-library metadata. No activity/significance threshold was imposed, so valid positive and negative control regions remain in the table.
Curation notes
The table is restricted to Type=Enhancer rows and includes 7,320 constructs present after the published barcode-level filtering/collapse. Activity scores are derived from medians of the supplied quantile-normalized counts and are not a reimplementation of the paper's sharpr2 regional FWER analysis. Appendix Table S1 driver indicators are repeated as locus-level annotations; they do not filter rows by biological activity. The raw GEO file also contains the SNP constructs and Jurkat samples.