Pwp2 promoter 10-bp tiling mutagenesis
CG dinucleotides enhance promoter activity independent of DNA methylationTrAC-seq assayed a Pwp2 promoter library containing 10-bp tiling-window mutants and transcription-factor motif controls in wild-type TC-1 mouse embryonic stem cells. The table provides replicate activity, WT-normalized activity, and DNA-supported barcode counts for each tiled construct.
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; wild-type TC-1 mouse embryonic stem cells
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 was subdivided into 10-bp tiling windows, each mutated in turn, alongside control constructs.
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 · 17 definitions
- element_id
- Unique Pwp2 construct identifier; labels encode the 10-bp tiled interval or control design.
- library
- Source expression library name.
- activity_rep1
- RNA/DNA barcode enrichment for biological replicate 1; source activity includes the study pseudocount.
- dna_barcodes_rep1
- Number of DNA-supported barcodes contributing to replicate 1 activity.
- activity_rep2
- RNA/DNA barcode enrichment for biological replicate 2; source activity includes the study pseudocount.
- dna_barcodes_rep2
- Number of DNA-supported barcodes contributing to replicate 2 activity.
- activity_rep3
- RNA/DNA barcode enrichment for biological replicate 3; source activity includes the study pseudocount.
- dna_barcodes_rep3
- Number of DNA-supported barcodes contributing to replicate 3 activity.
- relative_activity_rep1
- Activity relative to the WT construct in replicate 1, as supplied by GEO.
- relative_activity_rep2
- Activity relative to the WT construct in replicate 2, as supplied by GEO.
- relative_activity_rep3
- Activity relative to the WT construct in replicate 3, as supplied by GEO.
- activity_geomean
- Geometric mean of the non-missing per-replicate activity enrichments.
- log2_activity
- Mean log2-transformed activity enrichment across non-missing replicates.
- mean_dna_barcodes
- Arithmetic mean of numeric DNA-supported barcode counts across replicates.
- qc_replicates
- Number of replicates with activity and at least 3 DNA-supported barcodes; retained rows have at least 2.
- relative_activity_geomean
- Geometric mean of the non-missing WT-normalized activities.
- log2_relative_activity
- Mean log2-transformed WT-normalized activity across non-missing replicates.
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 element table, rows were retained only when activity and at least 3 DNA-supported barcodes were available in at least 2 of 3 biological replicates; all 45 of 45 source rows passed.
Curation notes
Input: raw_data/GSE116704_pwp2_lib4_results.tab.gz; GEO reporter samples GSM3258727-GSM3258733. The source file contains 45 rows and all passed the packaged QC. Relative-activity columns are source-provided ratios to the WT construct; promoter nucleotide sequences were not supplied in the public result table.