Snx3 promoter combinatorial CpG-depletion library
CG dinucleotides enhance promoter activity independent of DNA methylationTrAC-seq tested all combinations of CpG-mutated windows across the Snx3 promoter in wild-type TC-1 cells and matched Dnmt triple-knockout derivatives. The five-bit construct identifiers encode the promoter windows selected for CpG mutation, and the table retains source qPCR and methylation measurements where available.
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. Five Snx3 promoter windows were combinatorially kept wild type or mutated at CpGs, and the 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 · 40 definitions
- element_id
- Construct identifier; five-bit labels encode the Snx3 promoter windows selected for CpG mutation, with control labels retained as supplied.
- library
- Source expression library name.
- qpcr_activity
- Independent qPCR-based reporter activity measurement supplied for selected constructs; blank when unavailable.
- methylation_fraction
- Source methylation fraction for selected constructs, measured by bisulfite sequencing; blank when unavailable.
- gc_percent
- GC content of the tested promoter construct, in percent.
- cpg_percent
- CpG content of the tested promoter 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 2.
- 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 2.
- relative_activity_geomean_tko
- Geometric mean of Dnmt triple-knockout relative activities across replicates.
- log2_relative_activity_tko
- Mean log2-transformed Dnmt triple-knockout relative activity across 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. For this packaged matched-genotype table, rows were retained only when activity and at least 3 DNA-supported barcodes were available in at least 2 of 3 biological replicates in both WT and TKO; 33 of 44 source rows passed.
Curation notes
Input: raw_data/GSE116704_Snx3Lib1_results.tab.gz; GEO reporter samples GSM3258701-GSM3258713. The source file contains 44 rows; 33 matched rows passed the packaged QC. The TKO cells are CRISPR-engineered derivatives of TC-1 and do not have a separate Cellosaurus accession. Relative-activity, qPCR, and methylation fields are source-provided; promoter nucleotide sequences were not supplied in the public result table.