This pool is an independent collection of mouse genomic PPARγ motif-containing sequences used to test the motif-composition model, together with intact and motif-disrupted construct classes. The released counts were measured in differentiated 3T3-L1 adipocytes using matched RNA and plasmid-DNA barcode channels.
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
Region-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Differentiated 3T3-L1 adipocytes; no acute treatment
The construct names encode 145-bp-scale mouse genomic contexts centered on a 16-bp PPARγ/RXR motif, with intact and disrupted motif versions. Plasmids were transfected into differentiated 3T3-L1 adipocytes and harvested after 16 h for RNA-derived barcode and plasmid-DNA counting. The deposited Pool 3 matrices contain 15 barcode-count channels for each construct.
Processed data
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Visible columns (21 of 21)
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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 · 21 definitions
element_id
Original GEO construct name.
design_class
GEO prefix identifying the construct class (PPREwt, PPREwd, PPREct, or PPREcd).
genomic_context_id
Numeric genomic-site identifier encoded in the GEO name.
chromosome
Mouse chromosome encoded in the construct name.
start_mm9
Start coordinate of the central 16-bp 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
Remaining design suffix after the central motif; blank for the four basic Pool 3 classes.
genomic_binding_class
Bound or matched-unbound genomic context inferred from the Pool 3 construct prefix.
motif_state
Intact or disrupted central PPARγ motif inferred from the Pool 3 construct prefix.
barcode_count_or_channels
Number of deposited RNA/DNA barcode-count channels (15 for Pool 3).
positive_barcode_channels
Number of channels with both RNA and plasmid counts greater than zero.
rna_count
Sum of RNA-derived barcode counts across deposited channels.
plasmid_count
Sum of plasmid-DNA barcode counts across deposited channels.
rna_fraction
RNA count divided by the total RNA count across all source rows and channels.
plasmid_fraction
Plasmid count divided by the total plasmid count across all source rows and channels.
activity_log2
Median channel-level log2 RNA/DNA activity after per-channel library-size normalization.
activity_log2_from_summed_counts
Log2 RNA/DNA activity computed from the row-summed counts and aggregate library totals.
source_row
1-based line number in the downloaded source count file, including the header as line 1.
source_accession
GEO sample accessions supplying the RNA and plasmid matrices.
Quality control
GEO assigned perfect UTR-barcode matches to oligos and deposited counts for each barcode channel. Package QC retained 5,867 of 6,000 rows: at least 3 of 15 channels had both RNA and plasmid counts greater than zero, summed plasmid count was at least 100, summed RNA count was at least 10, and the median channel-level log2 RNA/DNA activity was finite. The 133 excluded rows were low-coverage in RNA, plasmid DNA, or informative channels. Activity fractions use library-size totals from the deposited matrix.
Curation notes
The source count matrix contains 6,000 rows and the four PPRE prefix classes were mapped to bound/unbound and intact/disrupted labels using the same naming convention as Pool 1. Rows with inadequate informative barcode coverage were removed from the packaged table.