The GEO series includes a Bank 2 LXRα no-ligand/T-compound reporter pair using the Library 2 oligo pool. This exploratory table reports count-normalized T-compound fold changes for the available pair; the publication and supplementary tables do not provide a DESeq2 analysis for these samples.
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
Human
Taxonomy ID
NCBITaxon:9606
Biosample
CVCL:0045
Reference genome
GRCm38/mm10
Design focus
Region-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
T-compound versus no ligand
This uses the same episomal pSTARRseq-ori SOSHI-seq Library 2 reporter pool and HEK293 transfection framework. The GEO metadata identifies the two conditions as Bank2 LXRα no T-compound and Bank2 LXRα with T-compound; it does not state the T-compound concentration or provide a replicate-based differential analysis. Values are calculated from the deposited per-fragment reporter-RNA counts and normalized to reads per million within each sample.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (18 of 18)
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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 · 18 definitions
fragment_number
Original numeric fragment number from the Library 2 description table.
element_id
Unique tested genomic fragment identifier (lib2-n).
chromosome
Mouse chromosome of the tested fragment.
start
Start coordinate of the tested fragment on GRCm38/mm10.
end
End coordinate of the tested fragment on GRCm38/mm10.
sequence
Tested mouse genomic insert sequence.
sequence_length_bp
Length of the tested insert in base pairs.
closest_gene
Closest annotated gene supplied by the study.
distance_to_tss_bp
Signed distance from the fragment to the closest gene transcription start site in base pairs.
second_closest_gene
Second closest annotated gene supplied by the study.
distance_to_second_tss_bp
Signed distance from the fragment to the second closest gene transcription start site in base pairs.
qc_min_count_all_files
Minimum raw reporter-RNA count between the two LXRα files; all rows are at least 10.
run42_lxr_no_ligand_count
Raw reporter-RNA count for RUN42, LXRα, no ligand (GSM9010794).
run42_lxr_t_compound_count
Raw reporter-RNA count for RUN42, LXRα, with T-compound (GSM9010795).
run42_lxr_no_ligand_rpm
No-ligand reporter-RNA count normalized to reads per million.
run42_lxr_t_compound_rpm
T-compound reporter-RNA count normalized to reads per million.
run42_lxr_fold_change
T-compound/no-ligand fold change based on RPM.
run42_lxr_log2_fold_change
Log2 of the T-compound/no-ligand RPM fold change.
Quality control
No paper-level QC or statistical test is reported for the GEO-only LXRα pair. As a transparent coverage filter, table.csv retains the 981 of 993 Library 2 fragments with at least 10 reads in both LXR count files; no significance or response-direction calls were invented.
Curation notes
This pair is present in the GSE298259 series design and deposited GEO sample files but is not described in the article narrative or Supplementary Table S2. It is therefore explicitly labeled exploratory and kept separate from the paper-reported TRα1/TRβ1 Library 2 experiment. The HEK293 biosample is human (CVCL:0045), while the tested insert sequences and coordinates are mouse.