This pool tests a matrix of PPARγ core motifs exchanged across 25 genomic flanking sequences, with additional control constructs. The released matrix was assayed in differentiated 3T3-L1 adipocytes and provides 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
Synthetic / Motif-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Differentiated 3T3-L1 adipocytes; no acute treatment
The manuscript describes 25 PPARγ core motifs swapped into 25 genomic flanking sequences; the deposited matrix includes the swap constructs and controls, for 1,350 source rows. Sequences were cloned into the minimal-promoter/luc2 plasmid reporter, transfected into differentiated 3T3-L1 adipocytes, and measured after 16 h by RNA-derived barcode counts relative to plasmid DNA. The released Pool 2 matrices contain 20 deposited barcode-count channels per construct.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (22 of 22)
Row
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
Page 1 · 50 rows · More results available
Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.
Column dictionary · 22 definitions
element_id
Original GEO construct name.
design_class
GEO construct prefix; Pool 2 entries are PPREwt.
genomic_context_id
Identifier for the genomic flanking sequence encoded in the GEO name.
chromosome
Mouse chromosome of the genomic flanking sequence.
start_mm9
Start coordinate of the central motif in the genomic flanking sequence.
end_mm9
End coordinate of the central motif as encoded in the GEO name; the source coordinate convention is retained.
strand
Strand of the genomic flanking sequence.
pparg_motif
Central motif sequence encoded in the GEO name for the flanking context.
design_detail
Raw suffix describing the inserted motif or control condition.
core_motif_id
Numeric core-motif identifier parsed from swap suffixes of the form <ID>_bound0 or <ID>_bound5; blank for controls.
swap_condition
Raw bound0/bound5 or bound0_mod/bound5_mod condition token for core-motif swap constructs.
control_type
core_motif_swap for parsed swap constructs; otherwise the raw control suffix.
barcode_count_or_channels
Number of deposited RNA/DNA barcode-count channels (20 for Pool 2).
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 all 1,350 of 1,350 rows: at least 3 of 20 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. Activity fractions use library-size totals from the deposited matrix.
Curation notes
The numeric core_motif_id and bound0/bound5[_mod] fields are parsed from the released construct names without assigning an unstated biological meaning to the condition token. The deposited matrix contains 1,350 rows, including controls, while the main-text schematic emphasizes the 625 swap combinations.