Pwp2 promoter CpG-window and TF-motif mutants
CG dinucleotides enhance promoter activity independent of DNA methylationTrAC-seq measured a combinatorial Pwp2 promoter mutant library in wild-type TC-1 cells and matched Dnmt triple-knockout derivatives. The library includes CpG-window combinations and targeted GABPA, NRF1, SP1/SP3, and MYC motif mutations, with source-provided WT-normalized activity.
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; matched wild-type and Dnmt1/Dnmt3a/Dnmt3b triple-knockout TC-1 derivatives
TrAC-seq used pooled promoter-barcode cassettes inserted by recombinase-mediated cassette exchange into the beta-globin locus. RNA/cDNA and genomic-DNA barcodes were sequenced separately; per-barcode RNA/DNA enrichment used the study pseudocount alpha=0.05 and was summarized across barcodes and three biological replicates. Pwp2 mutants alter CpG-containing windows or selected transcription-factor motifs, and the same library was assayed in WT and Dnmt triple-knockout cells.
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 · 38 definitions
- element_id
- Unique Pwp2 construct identifier describing the promoter-window or transcription-factor motif mutation.
- library
- Source expression library name.
- gc_percent
- GC content of the tested Pwp2 construct, in percent.
- cpg_percent
- CpG content of the tested Pwp2 construct, as reported by the source.
- cpg_observed_expected
- Observed-over-expected CpG density (OE) for the construct.
- cpg_sites
- Number of CpG sites in the construct.
- activity_wt_rep1
- WT RNA/DNA barcode enrichment for biological replicate 1; source activity includes the study pseudocount.
- dna_barcodes_wt_rep1
- Number of WT DNA-supported barcodes contributing to replicate 1 activity.
- activity_wt_rep2
- WT RNA/DNA barcode enrichment for biological replicate 2; source activity includes the study pseudocount.
- dna_barcodes_wt_rep2
- Number of WT DNA-supported barcodes contributing to replicate 2 activity.
- activity_wt_rep3
- WT RNA/DNA barcode enrichment for biological replicate 3; source activity includes the study pseudocount.
- dna_barcodes_wt_rep3
- Number of WT DNA-supported barcodes contributing to replicate 3 activity.
- activity_tko_rep1
- Dnmt triple-knockout RNA/DNA barcode enrichment for biological replicate 1; source activity includes the study pseudocount.
- dna_barcodes_tko_rep1
- Number of Dnmt triple-knockout DNA-supported barcodes contributing to replicate 1 activity.
- activity_tko_rep2
- Dnmt triple-knockout RNA/DNA barcode enrichment for biological replicate 2; source activity includes the study pseudocount.
- dna_barcodes_tko_rep2
- Number of Dnmt triple-knockout DNA-supported barcodes contributing to replicate 2 activity.
- activity_tko_rep3
- Dnmt triple-knockout RNA/DNA barcode enrichment for biological replicate 3; source activity includes the study pseudocount.
- dna_barcodes_tko_rep3
- Number of Dnmt triple-knockout DNA-supported barcodes contributing to replicate 3 activity.
- relative_activity_wt_rep1
- WT activity relative to the WT construct in replicate 1, as supplied by GEO.
- relative_activity_wt_rep2
- WT activity relative to the WT construct in replicate 2, as supplied by GEO.
- relative_activity_wt_rep3
- WT activity relative to the WT construct in replicate 3, as supplied by GEO.
- relative_activity_tko_rep1
- Dnmt triple-knockout activity relative to the WT construct in replicate 1, as supplied by GEO.
- relative_activity_tko_rep2
- Dnmt triple-knockout activity relative to the WT construct in replicate 2, as supplied by GEO.
- relative_activity_tko_rep3
- Dnmt triple-knockout activity relative to the WT construct in replicate 3, as supplied by GEO.
- activity_geomean_wt
- Geometric mean of non-missing WT activity enrichments across replicates.
- log2_activity_wt
- Mean log2-transformed WT activity enrichment across non-missing replicates.
- mean_dna_barcodes_wt
- Arithmetic mean of WT DNA-supported barcode counts across replicates.
- qc_replicates_wt
- WT replicates with activity and at least 3 DNA-supported barcodes; retained rows have at least 1 under the paper's Pwp2lib3 exception.
- relative_activity_geomean_wt
- Geometric mean of WT relative activities across non-missing replicates.
- log2_relative_activity_wt
- Mean log2-transformed WT relative activity across non-missing replicates.
- activity_geomean_tko
- Geometric mean of non-missing Dnmt triple-knockout activity enrichments across replicates.
- log2_activity_tko
- Mean log2-transformed Dnmt triple-knockout activity enrichment across non-missing replicates.
- mean_dna_barcodes_tko
- Arithmetic mean of Dnmt triple-knockout DNA-supported barcode counts across replicates.
- qc_replicates_tko
- Dnmt triple-knockout replicates with activity and at least 3 DNA-supported barcodes; retained rows have at least 1 under the paper's Pwp2lib3 exception.
- relative_activity_geomean_tko
- Geometric mean of Dnmt triple-knockout relative activities across non-missing replicates.
- log2_relative_activity_tko
- Mean log2-transformed Dnmt triple-knockout relative activity across non-missing replicates.
- log2_activity_tko_minus_wt
- Difference between TKO and WT mean log2 raw activity enrichments.
- log2_relative_activity_tko_minus_wt
- Difference between TKO and WT mean log2 relative activities.
Quality control
The paper retained uniquely assigned promoter barcodes (or assignments with second-most abundant sequence / most abundant sequence <0.3), required >20 normalized genomic-DNA reads per barcode, assigned absent RNA observations zero counts, and used alpha=0.05. The paper specifies a relaxed Pwp2lib3 element threshold of at least 1 of 3 replicates with at least 3 DNA-supported barcodes; for this packaged matched-genotype table that criterion was required in both WT and TKO. 30 of 34 source rows passed.
Curation notes
Input: raw_data/GSE116704_pwp2_lib3_results.tab.gz; GEO reporter samples GSM3258714-GSM3258726. The source file contains 34 rows; 30 matched rows passed the paper's relaxed Pwp2lib3 QC in both genotypes. Relative-activity columns are source-provided ratios to the WT construct; the TKO cells are CRISPR-engineered TC-1 derivatives without a separate Cellosaurus accession.