Lentiviral MPRA of CHIP-associated noncoding variants in CD34+ MUTZ-3 cells
Systematic functional dissection of germline noncoding risk variants impacting clonal hematopoiesisA 250-bp allele-paired library tested 687 CHIP-associated variants (reference and alternate alleles) plus positive and negative controls in the primitive CD34+ fraction of MUTZ-3 cells. Five biological replicates were measured by barcode RNA and genomic-DNA UMI counts 48 hours after lentiviral transduction; this package contains the QC-filtered paired-variant subset.
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
Basal / Untreated
The library used 250-bp genomic inserts centered on each allele, 15-bp flanking adapters, and 20-bp barcode tags in the pLS-SceI:MPRAv3-MCS lentiviral MPRA backbone with a minimal promoter/GFP reporter. CD34+ MUTZ-3 cells were transduced at MOI 33, harvested 48 hours later, and reporter RNA and integrated-library DNA barcode UMIs were sequenced. The paper analyzed these data with MPRASuite and MPRAnalyze; the packaged activity values are transparent count-derived log2 RNA/DNA summaries reconstructed from the deposited GEO count table.
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 · 59 definitions
- variant_id
- Variant coordinate and alleles in chr:position:reference>alternate format.
- chromosome
- Chromosome of the tested variant, using the chr-prefixed GRCh38 naming convention.
- position
- 1-based GRCh38 coordinate of the tested variant.
- reference_allele
- Reference allele represented by the oligo identifier suffix R.
- alternate_allele
- Alternate allele represented by the oligo identifier suffix A.
- reference_oligo_id
- Deposited Oligo identifier for the reference allele construct.
- alternate_oligo_id
- Deposited Oligo identifier for the alternate allele construct.
- reference_paired_barcode_count_r1
- Distinct reference-allele barcodes with >0 RNA and >0 DNA UMI counts in replicate 1 after mapping QC.
- reference_paired_barcode_count_r2
- Distinct reference-allele barcodes with >0 RNA and >0 DNA UMI counts in replicate 2 after mapping QC.
- reference_paired_barcode_count_r3
- Distinct reference-allele barcodes with >0 RNA and >0 DNA UMI counts in replicate 3 after mapping QC.
- reference_paired_barcode_count_r4
- Distinct reference-allele barcodes with >0 RNA and >0 DNA UMI counts in replicate 4 after mapping QC.
- reference_paired_barcode_count_r5
- Distinct reference-allele barcodes with >0 RNA and >0 DNA UMI counts in replicate 5 after mapping QC.
- alternate_paired_barcode_count_r1
- Distinct alternate-allele barcodes with >0 RNA and >0 DNA UMI counts in replicate 1 after mapping QC.
- alternate_paired_barcode_count_r2
- Distinct alternate-allele barcodes with >0 RNA and >0 DNA UMI counts in replicate 2 after mapping QC.
- alternate_paired_barcode_count_r3
- Distinct alternate-allele barcodes with >0 RNA and >0 DNA UMI counts in replicate 3 after mapping QC.
- alternate_paired_barcode_count_r4
- Distinct alternate-allele barcodes with >0 RNA and >0 DNA UMI counts in replicate 4 after mapping QC.
- alternate_paired_barcode_count_r5
- Distinct alternate-allele barcodes with >0 RNA and >0 DNA UMI counts in replicate 5 after mapping QC.
- reference_rna_count_r1
- Sum of reference-allele RNA UMI counts over paired barcodes in replicate 1.
- reference_rna_count_r2
- Sum of reference-allele RNA UMI counts over paired barcodes in replicate 2.
- reference_rna_count_r3
- Sum of reference-allele RNA UMI counts over paired barcodes in replicate 3.
- reference_rna_count_r4
- Sum of reference-allele RNA UMI counts over paired barcodes in replicate 4.
- reference_rna_count_r5
- Sum of reference-allele RNA UMI counts over paired barcodes in replicate 5.
- alternate_rna_count_r1
- Sum of alternate-allele RNA UMI counts over paired barcodes in replicate 1.
- alternate_rna_count_r2
- Sum of alternate-allele RNA UMI counts over paired barcodes in replicate 2.
- alternate_rna_count_r3
- Sum of alternate-allele RNA UMI counts over paired barcodes in replicate 3.
- alternate_rna_count_r4
- Sum of alternate-allele RNA UMI counts over paired barcodes in replicate 4.
- alternate_rna_count_r5
- Sum of alternate-allele RNA UMI counts over paired barcodes in replicate 5.
- reference_dna_count_r1
- Sum of reference-allele genomic-DNA UMI counts over paired barcodes in replicate 1.
- reference_dna_count_r2
- Sum of reference-allele genomic-DNA UMI counts over paired barcodes in replicate 2.
- reference_dna_count_r3
- Sum of reference-allele genomic-DNA UMI counts over paired barcodes in replicate 3.
- reference_dna_count_r4
- Sum of reference-allele genomic-DNA UMI counts over paired barcodes in replicate 4.
- reference_dna_count_r5
- Sum of reference-allele genomic-DNA UMI counts over paired barcodes in replicate 5.
- alternate_dna_count_r1
- Sum of alternate-allele genomic-DNA UMI counts over paired barcodes in replicate 1.
- alternate_dna_count_r2
- Sum of alternate-allele genomic-DNA UMI counts over paired barcodes in replicate 2.
- alternate_dna_count_r3
- Sum of alternate-allele genomic-DNA UMI counts over paired barcodes in replicate 3.
- alternate_dna_count_r4
- Sum of alternate-allele genomic-DNA UMI counts over paired barcodes in replicate 4.
- alternate_dna_count_r5
- Sum of alternate-allele genomic-DNA UMI counts over paired barcodes in replicate 5.
- reference_activity_log2_rna_dna_r1
- Reference-allele log2 RNA/DNA activity in replicate 1; RNA and DNA are library-size normalized using paired-barcode totals.
- reference_activity_log2_rna_dna_r2
- Reference-allele log2 RNA/DNA activity in replicate 2; RNA and DNA are library-size normalized using paired-barcode totals.
- reference_activity_log2_rna_dna_r3
- Reference-allele log2 RNA/DNA activity in replicate 3; RNA and DNA are library-size normalized using paired-barcode totals.
- reference_activity_log2_rna_dna_r4
- Reference-allele log2 RNA/DNA activity in replicate 4; RNA and DNA are library-size normalized using paired-barcode totals.
- reference_activity_log2_rna_dna_r5
- Reference-allele log2 RNA/DNA activity in replicate 5; RNA and DNA are library-size normalized using paired-barcode totals.
- alternate_activity_log2_rna_dna_r1
- Alternate-allele log2 RNA/DNA activity in replicate 1; RNA and DNA are library-size normalized using paired-barcode totals.
- alternate_activity_log2_rna_dna_r2
- Alternate-allele log2 RNA/DNA activity in replicate 2; RNA and DNA are library-size normalized using paired-barcode totals.
- alternate_activity_log2_rna_dna_r3
- Alternate-allele log2 RNA/DNA activity in replicate 3; RNA and DNA are library-size normalized using paired-barcode totals.
- alternate_activity_log2_rna_dna_r4
- Alternate-allele log2 RNA/DNA activity in replicate 4; RNA and DNA are library-size normalized using paired-barcode totals.
- alternate_activity_log2_rna_dna_r5
- Alternate-allele log2 RNA/DNA activity in replicate 5; RNA and DNA are library-size normalized using paired-barcode totals.
- allelic_effect_log2_alt_vs_ref_r1
- Alternate activity minus reference activity in replicate 1.
- allelic_effect_log2_alt_vs_ref_r2
- Alternate activity minus reference activity in replicate 2.
- allelic_effect_log2_alt_vs_ref_r3
- Alternate activity minus reference activity in replicate 3.
- allelic_effect_log2_alt_vs_ref_r4
- Alternate activity minus reference activity in replicate 4.
- allelic_effect_log2_alt_vs_ref_r5
- Alternate activity minus reference activity in replicate 5.
- reference_activity_log2_mean
- Mean reference-allele log2 RNA/DNA activity across the five replicates.
- alternate_activity_log2_mean
- Mean alternate-allele log2 RNA/DNA activity across the five replicates.
- allelic_effect_log2_alt_vs_ref_mean
- Mean alternate-minus-reference log2 RNA/DNA effect across the five replicates.
- allelic_effect_log2_alt_vs_ref_sd
- Sample standard deviation of the five replicate alternate-minus-reference effects.
- allelic_effect_log2_alt_vs_ref_min
- Minimum alternate-minus-reference log2 effect among the five replicates.
- allelic_effect_log2_alt_vs_ref_max
- Maximum alternate-minus-reference log2 effect among the five replicates.
- replicates_passed_qc
- Number of biological replicates retained after the paired-barcode oligo QC filter.
Quality control
The paper discarded oligo-barcode alignments with >5% mapping error, removed barcode observations lacking both RNA and DNA counts within a replicate, and removed oligos with 2 or fewer paired barcodes in any replicate. For this package, Error <= 0.05 was retained, paired RNA/DNA barcode observations were aggregated separately for each replicate, and only complete reference/alternate variant pairs whose two oligos each had >2 paired barcodes in all five replicates were retained. This yielded 668 variant pairs from 672 complete captured pairs. ORF negative controls, positive controls, NA:NA constructs, wC conflict-flagged constructs, and incomplete allele pairs were excluded from the variant-focused table.
Curation notes
The source is the MPRA-specific processed count table deposited under GEO series GSE336143; raw sequencing reads from the GEO archive were intentionally not packaged. The paper reports 1,588 captured constructs and 672 variants for the allelic analysis, while this deposited table contains 1,587 unique oligos and 672 complete reference/alternate pairs. Four complete pairs failed the paper's >2 paired barcodes per oligo per replicate rule, leaving 668 rows. The deposited Oligo IDs use R/A suffixes, which were used to pair alleles; rs identifiers, nearest-gene annotations, and the paper's MPRAnalyze q-values were not present in this count file and were not inferred. Activity and allelic-effect columns are count-derived summaries, not reimplementations of the paper's MPRAnalyze model or Storey q-values. The paper's Methods say six independent transductions, but the results, figure captions, and deposited count table contain five MPRA replicates; five were therefore used here.