This pool substitutes correlated TF motifs into existing motif sites within active PPARγ-bound genomic enhancer backgrounds. The GEO release supplies oligo-level RNA and plasmid counts summed across assigned barcodes, with target and inserted motif tokens parsed from each construct name.
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.
Organism
Mouse
Taxonomy ID
NCBITaxon:10090
Biosample
CVCL:0123
Reference genome
mm9
Design focus
Synthetic / Motif-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Differentiated 3T3-L1 adipocytes; no acute treatment
The manuscript describes substitution of each of 38 correlated TF consensus motifs into existing sites in bound genomic sequences. The GEO Pool 6 matrix contains oligo-level tags, counts.rna, and counts.plasmid, where the count fields are summed across barcode assignments; constructs were assayed in differentiated 3T3-L1 adipocytes after a 16-h expression period.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (23 of 23)
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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; Pool 6 entries are PPREwt.
genomic_context_id
Identifier for the bound genomic enhancer background.
chromosome
Mouse chromosome encoded in the construct name.
start_mm9
Start coordinate of the central motif as encoded in the GEO name.
end_mm9
End coordinate of the central motif as encoded in the GEO name; the source coordinate convention is retained.
strand
Strand of the source genomic motif.
pparg_motif
Central 16-bp PPARγ/RXR motif sequence encoded in the GEO name.
design_detail
Raw substitution suffix, generally target_motif_target_start_target_end_inserted_motif.
target_motif_name
Motif token associated with the existing target site in the raw suffix.
target_start
Start position of the substituted target site encoded in the raw suffix.
target_end
End position of the substituted target site encoded in the raw suffix.
inserted_motif_name
TF motif token substituted into the target site.
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 6 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 6.
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 6 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 3,715 of 3,720 source rows with tags at least 3, plasmid count at least 100, and RNA count at least 10. Five low-coverage rows were excluded; activity is a library-size-normalized log2 RNA/plasmid ratio from aggregate counts.
Curation notes
The target and inserted motif fields are mechanical parses of the released names and the complete suffix remains in design_detail. The processed table follows the 3,720-row GEO aggregate file; reported construct totals in the manuscript and deposited file are not identical.