Allele-specific 150-bp TNFAIP3-locus oligos were assayed in Jurkat Clone E6-1 human immune cells after 2.5 ug/ml anti-cd3 + 10 ng/ml pma for 1 hour using an episomal plasmid MPRA. 3 biological replicates are represented in the deposited matrix.
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
Variant-focused
Region of interest
chr6:137846078-138453052
Perturbation & assay details
2.5 ug/mL anti-CD3 + 10 ng/mL PMA for 1 hour
The library used synthesized 150-bp genomic allele contexts with a 20-bp barcode and approximately 250 DNA barcodes per allele, placed upstream of the TNFAIP3 promoter driving GFP with the barcode in the reporter 3-prime UTR. Transfection retained the reporter on an extrachromosomal plasmid. GEO source accessions: GSM4055642, GSM4055644, GSM4055646.
Processed data
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Column dictionary · 58 definitions
snp_id
Variant identifier used by Supplementary Data 9; generally an rsID.
allele_a
Allele A in the authors' comparison, in genomic orientation from the probe map.
allele_b
Allele B in the authors' comparison, in genomic orientation from the probe map.
chromosome
Chromosome containing the TNFAIP3 locus, formatted as chr6.
position_hg19
Variant coordinate on hg19.
in_tad
Supplementary Data 3 indicator that the variant is in the TNFAIP3 disease-associated TAD.
eas_haplotype
Supplementary Data 3 East Asian haplotype tag, if available.
eur_haplotype
Supplementary Data 3 European haplotype tag, if available.
gwas_tag_snp
Supplementary Data 3 GWAS tag-SNP identifier(s) associated with this variant, if available.
gwas_disease
Disease/trait annotation from Supplementary Data 3.
gwas_study
GWAS study annotation from Supplementary Data 3.
gwas_ld_r2
LD R-squared annotation from Supplementary Data 3.
fine_mapping_traits_95cs
Fine-mapping 95% credible-set trait annotations from Supplementary Data 3.
fine_mapping_traits_pip_gt_10
Fine-mapping trait annotations with posterior inclusion probability >0.10 from Supplementary Data 3.
rs_snp_aliases_a
Semicolon-separated rsSNP aliases from probe-map rows associated with allele A.
rs_snp_aliases_b
Semicolon-separated rsSNP aliases from probe-map rows associated with allele B.
allele_a_probe_count
Number of unique designed probes mapped to SNP/allele A.
allele_b_probe_count
Number of unique designed probes mapped to SNP/allele B.
allele_a_probe_ids
Semicolon-separated designed probe IDs mapped to SNP/allele A.
allele_b_probe_ids
Semicolon-separated designed probe IDs mapped to SNP/allele B.
replicate_count
Number of source biological replicates for this experiment.
source_sample_accessions
Semicolon-separated GEO sample accessions for the source replicates.
published_mpra_hit_from_data3
Authors' condition-specific MPRA hit call from Supplementary Data 3.
mpra_hit_paper_criterion
Package check of the paper criterion: at least two q-values <0.1 and consistent allelic-skew direction; blank when deposited q-values are incomplete.
valid_q_replicates
Number of source replicates with a finite deposited Data9 FDR q-value.
allele_a_good_tag_count_rep1
Allele A barcode tags passing input >=30 and RNA >=4 thresholds in source replicate 1.
allele_b_good_tag_count_rep1
Allele B barcode tags passing input >=30 and RNA >=4 thresholds in source replicate 1.
allele_a_input_count_rep1
Sum DNA/input counts across passing allele A tags in source replicate 1.
allele_b_input_count_rep1
Sum DNA/input counts across passing allele B tags in source replicate 1.
allele_a_rna_count_rep1
Sum RNA/output counts across passing allele A tags in source replicate 1.
allele_b_rna_count_rep1
Sum RNA/output counts across passing allele B tags in source replicate 1.
allele_a_raw_mean_log2_rna_dna_rep1
Mean tag-level log2(RNA/input) for passing allele A tags in source replicate 1; not GC-normalized.
allele_b_raw_mean_log2_rna_dna_rep1
Mean tag-level log2(RNA/input) for passing allele B tags in source replicate 1; not GC-normalized.
allelic_skew_log2_rep1
Deposited Supplementary Data 9 allelic skew for replicate 1, allele A minus allele B after author normalization.
p_value_rep1
Deposited uncorrected two-sided t-test P-value for replicate 1.
fdr_q_rep1
Deposited Benjamini-Hochberg FDR q-value for replicate 1.
allele_a_good_tag_count_rep2
Allele A barcode tags passing input >=30 and RNA >=4 thresholds in source replicate 2.
allele_b_good_tag_count_rep2
Allele B barcode tags passing input >=30 and RNA >=4 thresholds in source replicate 2.
allele_a_input_count_rep2
Sum DNA/input counts across passing allele A tags in source replicate 2.
allele_b_input_count_rep2
Sum DNA/input counts across passing allele B tags in source replicate 2.
allele_a_rna_count_rep2
Sum RNA/output counts across passing allele A tags in source replicate 2.
allele_b_rna_count_rep2
Sum RNA/output counts across passing allele B tags in source replicate 2.
allele_a_raw_mean_log2_rna_dna_rep2
Mean tag-level log2(RNA/input) for passing allele A tags in source replicate 2; not GC-normalized.
allele_b_raw_mean_log2_rna_dna_rep2
Mean tag-level log2(RNA/input) for passing allele B tags in source replicate 2; not GC-normalized.
allelic_skew_log2_rep2
Deposited Supplementary Data 9 allelic skew for replicate 2, allele A minus allele B after author normalization.
p_value_rep2
Deposited uncorrected two-sided t-test P-value for replicate 2.
fdr_q_rep2
Deposited Benjamini-Hochberg FDR q-value for replicate 2.
allele_a_good_tag_count_rep3
Allele A barcode tags passing input >=30 and RNA >=4 thresholds in source replicate 3.
allele_b_good_tag_count_rep3
Allele B barcode tags passing input >=30 and RNA >=4 thresholds in source replicate 3.
allele_a_input_count_rep3
Sum DNA/input counts across passing allele A tags in source replicate 3.
allele_b_input_count_rep3
Sum DNA/input counts across passing allele B tags in source replicate 3.
allele_a_rna_count_rep3
Sum RNA/output counts across passing allele A tags in source replicate 3.
allele_b_rna_count_rep3
Sum RNA/output counts across passing allele B tags in source replicate 3.
allele_a_raw_mean_log2_rna_dna_rep3
Mean tag-level log2(RNA/input) for passing allele A tags in source replicate 3; not GC-normalized.
allele_b_raw_mean_log2_rna_dna_rep3
Mean tag-level log2(RNA/input) for passing allele B tags in source replicate 3; not GC-normalized.
allelic_skew_log2_rep3
Deposited Supplementary Data 9 allelic skew for replicate 3, allele A minus allele B after author normalization.
p_value_rep3
Deposited uncorrected two-sided t-test P-value for replicate 3.
fdr_q_rep3
Deposited Benjamini-Hochberg FDR q-value for replicate 3.
Quality control
Paper QC excluded tags with <30 DNA/input or <4 RNA/output reads, median/GC-normalized log RNA/DNA, removed eight blacklisted 5-mers, and used two-sided t-tests with BH FDR. Package QC retained 2,577 of 2,744 Data9 allele pairs after requiring finite P/skew in all 3 source replicates, at least one passing tag per allele, and >=80 combined passing tags per replicate. Deposited Q values, including missing values, are preserved. The blacklist sequences are not separately released, so raw means are count-thresholded summaries rather than paper-normalized effect sizes.
Curation notes
Source group Jurkat_stim_transfection has 3 biological replicates. Data9 statistics are joined to the map through old_SNPID and genomic-orientation alleles; rsSNP is retained as an alias. GEO also lists BJAB transfection sample records, but no corresponding columns occur in the released matrix or Data9, so no unsupported BJAB transfection experiment was created. Sequence-level oligos and barcode associations remain in raw_data.