Housekeeping-promoter CpG mutants in WT and Dnmt triple-knockout cells
CG dinucleotides enhance promoter activity independent of DNA methylationTrAC-seq compared CpG-depleted mutant versions of mouse housekeeping promoters in wild-type TC-1 cells and matched Dnmt1/Dnmt3a/Dnmt3b triple-knockout derivatives. Each construct is annotated with its promoter coordinates, CpG mutation percentage, sequence composition, and WT/TKO 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. CpGs outside selected bound transcription-factor motifs were mutated, 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.
Visible columns (43 of 43)
| Row | |||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | |||||||||||||||||||||||||||||||||||||||||||
| 2 | |||||||||||||||||||||||||||||||||||||||||||
| 3 | |||||||||||||||||||||||||||||||||||||||||||
| 4 | |||||||||||||||||||||||||||||||||||||||||||
| 5 | |||||||||||||||||||||||||||||||||||||||||||
| 6 | |||||||||||||||||||||||||||||||||||||||||||
| 7 | |||||||||||||||||||||||||||||||||||||||||||
| 8 | |||||||||||||||||||||||||||||||||||||||||||
| 9 | |||||||||||||||||||||||||||||||||||||||||||
| 10 | |||||||||||||||||||||||||||||||||||||||||||
| 11 | |||||||||||||||||||||||||||||||||||||||||||
| 12 | |||||||||||||||||||||||||||||||||||||||||||
| 13 | |||||||||||||||||||||||||||||||||||||||||||
| 14 | |||||||||||||||||||||||||||||||||||||||||||
| 15 | |||||||||||||||||||||||||||||||||||||||||||
| 16 | |||||||||||||||||||||||||||||||||||||||||||
| 17 | |||||||||||||||||||||||||||||||||||||||||||
| 18 | |||||||||||||||||||||||||||||||||||||||||||
| 19 | |||||||||||||||||||||||||||||||||||||||||||
| 20 | |||||||||||||||||||||||||||||||||||||||||||
| 21 | |||||||||||||||||||||||||||||||||||||||||||
| 22 | |||||||||||||||||||||||||||||||||||||||||||
| 23 | |||||||||||||||||||||||||||||||||||||||||||
| 24 | |||||||||||||||||||||||||||||||||||||||||||
| 25 | |||||||||||||||||||||||||||||||||||||||||||
| 26 | |||||||||||||||||||||||||||||||||||||||||||
| 27 | |||||||||||||||||||||||||||||||||||||||||||
| 28 | |||||||||||||||||||||||||||||||||||||||||||
| 29 | |||||||||||||||||||||||||||||||||||||||||||
| 30 | |||||||||||||||||||||||||||||||||||||||||||
| 31 | |||||||||||||||||||||||||||||||||||||||||||
| 32 | |||||||||||||||||||||||||||||||||||||||||||
| 33 | |||||||||||||||||||||||||||||||||||||||||||
| 34 | |||||||||||||||||||||||||||||||||||||||||||
| 35 | |||||||||||||||||||||||||||||||||||||||||||
| 36 | |||||||||||||||||||||||||||||||||||||||||||
| 37 | |||||||||||||||||||||||||||||||||||||||||||
| 38 | |||||||||||||||||||||||||||||||||||||||||||
| 39 | |||||||||||||||||||||||||||||||||||||||||||
| 40 | |||||||||||||||||||||||||||||||||||||||||||
| 41 | |||||||||||||||||||||||||||||||||||||||||||
| 42 | |||||||||||||||||||||||||||||||||||||||||||
| 43 | |||||||||||||||||||||||||||||||||||||||||||
| 44 | |||||||||||||||||||||||||||||||||||||||||||
| 45 | |||||||||||||||||||||||||||||||||||||||||||
| 46 | |||||||||||||||||||||||||||||||||||||||||||
| 47 | |||||||||||||||||||||||||||||||||||||||||||
| 48 | |||||||||||||||||||||||||||||||||||||||||||
| 49 | |||||||||||||||||||||||||||||||||||||||||||
| 50 |
Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.
Column dictionary · 43 definitions
- element_id
- Unique promoter construct identifier; the source label encodes chromosome, interval, strand, and mutation percentage.
- library
- Source expression library name.
- 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.
- chromosome
- Mouse chromosome of the source promoter interval.
- start
- Start coordinate of the source promoter interval in mm9.
- end
- End coordinate of the source promoter interval in mm9.
- strand
- Strand of the source promoter interval.
- cpg_mutation
- Percentage label for the fraction of designated CpGs mutated 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 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. 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; 51 of 60 source rows passed.
Curation notes
Input: raw_data/GSE116704_HKGlib3_results.tab.gz; GEO reporter samples GSM3258688-GSM3258700. The source file contains 60 construct rows; 51 matched rows passed the per-genotype packaged QC. The TKO cells are CRISPR-engineered derivatives of TC-1 and do not have a separate Cellosaurus accession. Relative-activity columns are source-provided ratios to the WT construct.