Chr21q22 MPRA enhancer and allelic activity in inflammatory macrophages
A disease-associated gene desert directs macrophage inflammation through ETS2An episomal MPRA library tested 114-nucleotide genomic sequences tiling the chr21q22 candidate-SNP region at 50-bp intervals, together with allele-specific constructs for candidate variants and control constructs. TPP macrophages from eight healthy donors were transfected; RNA was collected 24 hours later and compared with four input-DNA library 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.
Perturbation & assay details
Inflammatory TPP differentiation: GM-CSF for 3 days, followed by GM-CSF plus TNFα, PGE2, and Pam3CSK4 for 3 days; no additional MPRA treatment
The pGL4.10M-derived episomal reporter used an RSV promoter adapted for primary macrophages. Oligos contained a 16-nt universal primer site, 114-nt variable genomic sequence, KpnI/XbaI sites, an 11-nt barcode, and a 17-nt universal primer site. Tiling constructs had six unique barcodes; each allelic construct had 30 unique barcodes. Barcode libraries were sequenced as 50-bp single-end Illumina HiSeq 2500 reads from mRNA and input DNA.
Processed data
50 rows per page. Click a cell to inspect its full value.
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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
- element_id
- Source construct identifier.
- construct_type
- Source construct class: Enhancer or SNP.
- library_subtype
- Derived library class: target_tiling, target_allelic, positive_control, or negative_control.
- rs_id
- Source dbSNP or synthetic variant identifier; NA denotes not applicable.
- element_tag
- Source replicate/tiling tag (A, B, C, or NA).
- allele_label
- Source allele label: ref, alt, mult, or NA; nucleotide identities were not supplied in the barcode table.
- coordinate_hg19
- Source 114-nt construct interval on hg19, or NA:NA-NA for synthetic sequences.
- sequence_114nt
- 114-nt variable genomic or synthetic sequence used in the construct.
- source_barcode_count
- Number of barcode rows for the construct in the deposited barcode-count file before the CPM filter.
- qc_retained_barcode_count
- Number of source barcode rows meeting the reproduced median-CPM >=1 criterion in both mRNA and DNA groups.
- rna_1TPP_norm_count
- Deposited quantile-normalized, collapsed construct count for donor 1 TPP macrophage mRNA.
- rna_2TPP_norm_count
- Deposited quantile-normalized, collapsed construct count for donor 2 TPP macrophage mRNA.
- rna_3TPP_norm_count
- Deposited quantile-normalized, collapsed construct count for donor 3 TPP macrophage mRNA.
- rna_4TPP_norm_count
- Deposited quantile-normalized, collapsed construct count for donor 4 TPP macrophage mRNA.
- rna_5TPP_norm_count
- Deposited quantile-normalized, collapsed construct count for donor 5 TPP macrophage mRNA.
- rna_6TPP_norm_count
- Deposited quantile-normalized, collapsed construct count for donor 6 TPP macrophage mRNA.
- rna_7TPP_norm_count
- Deposited quantile-normalized, collapsed construct count for donor 7 TPP macrophage mRNA.
- rna_8TPP_norm_count
- Deposited quantile-normalized, collapsed construct count for donor 8 TPP macrophage mRNA.
- dna_DNAv1_norm_count
- Deposited quantile-normalized, collapsed construct count for input DNA replicate 1.
- dna_DNAv2_norm_count
- Deposited quantile-normalized, collapsed construct count for input DNA replicate 2.
- dna_DNAv3_norm_count
- Deposited quantile-normalized, collapsed construct count for input DNA replicate 3.
- dna_DNAv4_norm_count
- Deposited quantile-normalized, collapsed construct count for input DNA replicate 4.
- dna_mean_norm_count
- Arithmetic mean of the four deposited normalized input-DNA counts.
- dna_median_norm_count
- Median of the four deposited normalized input-DNA counts.
- rna_mean_norm_count
- Arithmetic mean of the eight deposited normalized mRNA counts.
- activity_mean_log2_rna_dna
- Mean across eight donors of log2(normalized mRNA count / mean normalized input-DNA count).
- activity_median_log2_rna_dna
- Median across eight donors of log2(normalized mRNA count / mean normalized input-DNA count).
- activity_sd_log2_rna_dna
- Sample standard deviation across eight donors of the donor-level log2 RNA/DNA activity values.
- activity_1TPP_log2_rna_dna
- Donor 1 log2(normalized mRNA count / mean normalized input-DNA count).
- activity_2TPP_log2_rna_dna
- Donor 2 log2(normalized mRNA count / mean normalized input-DNA count).
- activity_3TPP_log2_rna_dna
- Donor 3 log2(normalized mRNA count / mean normalized input-DNA count).
- activity_4TPP_log2_rna_dna
- Donor 4 log2(normalized mRNA count / mean normalized input-DNA count).
- activity_5TPP_log2_rna_dna
- Donor 5 log2(normalized mRNA count / mean normalized input-DNA count).
- activity_6TPP_log2_rna_dna
- Donor 6 log2(normalized mRNA count / mean normalized input-DNA count).
- activity_7TPP_log2_rna_dna
- Donor 7 log2(normalized mRNA count / mean normalized input-DNA count).
- activity_8TPP_log2_rna_dna
- Donor 8 log2(normalized mRNA count / mean normalized input-DNA count).
- variant_pair_ref_element_id
- Paired ref construct identifier for the same source rsID and element tag; blank when no ref/alt pair applies.
- variant_pair_alt_element_id
- Paired alt construct identifier for the same source rsID and element tag; blank when no ref/alt pair applies.
- variant_effect_alt_minus_ref_mean_log2
- Mean across eight donors of paired alt minus ref donor-level activity log2 values; descriptive derived contrast, not the paper's QuASAR-MPRA statistic.
- variant_effect_alt_minus_ref_median_log2
- Median across eight donors of paired alt minus ref donor-level activity log2 values.
- variant_effect_alt_minus_ref_sd_log2
- Sample standard deviation across eight donors of paired alt minus ref donor-level activity log2 values.
- variant_effect_n_donors
- Number of paired donor contrasts used for the derived alt-minus-ref summary.
- overlaps_paper_active_window
- True when the construct interval overlaps the paper-reported active enhancer focus chr21:40466236-40466677 (hg19).
- qc_status
- Inclusion status; every row is present in the deposited filtered normalized construct file.
Quality control
The study used FastQC v0.11.9, required a perfect library-barcode match followed by at least 10 bases of expected constant sequence, and considered a transfection successful when at least 70% of the oligonucleotide library had count >1. Barcodes with median counts per million <1 in either the mRNA or DNA samples were removed; identical constructs were collapsed and quantile normalized with normalize.quantiles from preprocessCore in R 4.1.0. The processed table retains the 382 construct rows in the deposited filtered normalized file and excludes the four raw elements absent from that file. No additional significance threshold was imposed on the derived activity values.
Curation notes
This is a mixed target library: the table preserves both the chr21q22 tiling enhancer constructs and allele-focused constructs, along with positive and negative controls. The paper reports a 442-bp active enhancer focus at chr21:40466236-40466677 (hg19), represented by the overlap flag. Source labels ref/alt/mult were retained exactly; no nucleotide or risk/non-risk mapping was inferred from the barcode table. The deposited normalized file has 382 rows, while the raw barcode file has 386 unique element IDs; four elements were excluded because they were not present in the deposited filtered construct table.