Pool 7: synthetic PPARγ enhancer motif combinations
Systematic dissection of genomic features determining transcription factor binding and enhancer functionThis pool tests synthetic enhancer constructs carrying individual or paired sites from 15 positively correlated TF motifs in multiple configurations on low-activity templates. The GEO release supplies oligo-level RNA and plasmid counts summed across assigned barcodes.
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
Differentiated 3T3-L1 adipocytes; no acute treatment
The manuscript describes adding sites for 15 positively correlated motifs individually and in pairs to three neutral templates in configurations containing two, four, or six total sites. The GEO Pool 7 matrix contains oligo-level tags, counts.rna, and counts.plasmid, where the count fields are summed across barcode assignments; the MAC construct names retain the mouse genomic coordinates of the template and the synthetic motif/configuration suffix.
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 · 23 definitions
- element_id
- Original GEO oligo name.
- design_class
- GEO construct prefix; MAC identifies the synthetic-template family.
- genomic_context_id
- Blank for MAC names because the synthetic construct naming convention has no separate context-ID token.
- chromosome
- Mouse chromosome of the template coordinate encoded in the construct name.
- start_mm9
- Start coordinate of the template's central motif as encoded in the GEO name.
- end_mm9
- End coordinate of the template's central motif as encoded in the GEO name; the source coordinate convention is retained.
- strand
- Strand of the template motif.
- pparg_motif
- Central 16-bp PPARγ/RXR motif sequence encoded in the GEO name.
- design_detail
- Raw synthetic motif/configuration suffix.
- synthetic_motif_1
- First TF motif token parsed from the synthetic suffix.
- synthetic_motif_2
- Second TF motif token parsed from the synthetic suffix; repeated tokens indicate the corresponding repeated motif design.
- site_configuration
- Numeric site-count/configuration token encoded in the raw suffix.
- replicate_number
- Final numeric configuration replicate token encoded in the raw suffix.
- barcode_count_or_channels
- GEO tags value: number of barcode-to-oligo assignments contributing to the aggregate counts.
- positive_barcode_channels
- Blank because the deposited Pool 7 counts are already summed across barcodes.
- rna_count
- GEO counts.rna value, summed across assigned barcodes.
- plasmid_count
- GEO counts.plasmid value, summed across assigned barcodes.
- rna_fraction
- RNA count divided by the total RNA count across all source rows.
- plasmid_fraction
- Plasmid count divided by the total plasmid count across all source rows.
- activity_log2
- Library-size-normalized log2 RNA/plasmid activity from aggregate counts.
- activity_log2_from_summed_counts
- Same aggregate-count activity score as activity_log2 for Pool 7.
- source_row
- 1-based line number in the downloaded source count file, including the header as line 1.
- source_accession
- GEO series accession supplying the aggregate Pool 7 matrix.
Quality control
GEO barcode reconstruction retained proper paired alignments with mapping score at least 25 and edit distance at most 5, and removed singleton or multiply matched barcodes. Package QC retained 2,987 of 3,243 source rows with tags at least 3, plasmid count at least 100, and RNA count at least 10. The 256 excluded rows were low-coverage, mostly with no RNA counts; activity is a library-size-normalized log2 RNA/plasmid ratio from aggregate counts.
Curation notes
MAC names use a six-token coordinate format without a separate genomic_context_id; the parser preserves their coordinates. The processed table follows the 3,243-row GEO aggregate file, whereas the manuscript's pool description reports a different total; no attempt was made to fabricate missing constructs.