This pool contains 750 mouse genomic PPARγ ChIP-seq-bound sites, 750 matched unbound sites, and native/motif-disrupted versions of each. The constructs were tested in differentiated 3T3-L1 adipocytes with matched plasmid-DNA and RNA barcode counts.
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 library used approximately 145-bp genomic sequences centered on a 16-bp PPARγ/RXR DR1 motif, cloned upstream of a minimal promoter and luc2 ORF with matched 3′ UTR barcodes. Plasmids were transfected into 3T3-L1 adipocytes seven days after differentiation, cells were grown for 16 h, and RNA-derived barcode counts were compared with plasmid-DNA counts. The deposited Pool 1 matrices contain nine 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 1 classes.
genomic_binding_class
Bound or matched-unbound genomic context inferred from the Pool 1 construct prefix.
motif_state
Intact or disrupted central PPARγ motif inferred from the Pool 1 construct prefix.
barcode_count_or_channels
Number of deposited RNA/DNA barcode-count channels (nine for Pool 1).
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, matching the paper's activity definition.
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 2,998 of 3,000 rows: at least 3 of 9 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. Two low-plasmid rows were excluded; activity fractions use library-size totals from the deposited matrix.
Curation notes
The prefix interpretation follows the Pool 1 schematic and the paired coordinates in the released names: PPREwt is bound/intact, PPREwd bound/disrupted, PPREct matched-unbound/intact, and PPREcd matched-unbound/disrupted. The processed table retains the raw labels and central motif coordinates; it does not include the separate PPARγ ChIP-seq counts.