The complete RSV-promoter plasmid library, containing both SNP allele constructs and 114-bp enhancer tiles, was transfected into Jurkat E6.1 cells in resting and stimulated states. This table reports construct-level median RNA/DNA activity derived from the GEO-supplied quantile-normalized collapsed counts for the four Jurkat RNA replicates per state.
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:0367
Reference genome
hg19
Design focus
Other
Region of interest
Not reported / not applicable
Perturbation & assay details
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
Jurkat E6.1 clone cells received the same episomal RSV-promoter/EGFP barcode MPRA library used in primary CD4 T cells. The mixed library included reference/alternate SNP constructs, multi-allelic combinations, enhancer tiles, and controls, each represented by 6 or 30 unique 11-nt barcodes according to construct class. Jurkat RNA was collected 24 hours after nucleofection and normalized to four input plasmid DNA library replicates.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (21 of 21)
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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 · 21 definitions
element_id
Unique barcode-library identifier for the retained construct.
construct_group_id
Allele-pair grouping identifier; reference/alternate SNP element IDs share the identifier after removing the final _ref or _alt suffix, while enhancer constructs group to themselves.
construct_type
Library construct class: SNP or Enhancer.
snp_id
SNP identifier from the barcode-library metadata; blank for enhancer constructs.
element_tag
A/B/C tile tag for SNP constructs; blank for enhancer constructs.
allele
Reference/alternate construct label for SNP constructs; blank for enhancer constructs.
coordinates_hg19
Inclusive genomic interval of the 114-bp tested sequence on hg19.
sequence_114bp
Synthesized oligonucleotide sequence tested in the MPRA.
sequence_length_bp
Length in base pairs of sequence_114bp.
library_barcode_count
Number of barcode-library rows assigned to the construct in the GEO raw barcode file; the design used 30 barcodes per SNP allele construct and 6 per enhancer construct.
dna_median_quantile_normalized_count
Median of v1-v4 input plasmid DNA construct counts from the GEO quantile-normalized collapsed table.
Median of the four stimulated Jurkat RNA construct counts from the GEO quantile-normalized collapsed table.
stimulated_jurkat_rna_over_dna
Stimulated Jurkat median RNA construct count divided by the median input DNA construct count.
stimulated_jurkat_log2_rna_over_dna
Base-2 logarithm of stimulated_jurkat_rna_over_dna; a derived construct activity score.
n_jurkat_resting_replicates
Number of resting Jurkat RNA replicates summarized (4).
n_jurkat_stimulated_replicates
Number of stimulated Jurkat RNA replicates summarized (4).
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 used for the derived Jurkat summaries.
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 table retains all 9,109 constructs present in the authors' GEO normalized/collapsed post-QC file. Median Jurkat RNA/DNA ratios and log2 scores are derived summaries; no additional significance filter was applied.
Curation notes
This child preserves the Jurkat comparison arm as a mixed SNP/tiling construct table. It contains 9,109 post-QC construct rows and reports derived activity summaries rather than QuASAR-MPRA allele-specific P/q values; the published EV2/EV3 inferential tables were generated for the primary CD4 T-cell conditions. The Jurkat cell line is mapped to Cellosaurus CVCL:0367 (Jurkat E6.1).