Murine Tbx3/Tbx5 locus STARR-seq HeLa pilot

GEO includes a single-replicate murine STARR-seq pilot in HeLa cells with plasmid-input, pcDNA-control RNA, and SG4-response RNA BigWig tracks. Because no HeLa BED call file was deposited, the processed table derives 50-bp response bins from the three public BigWigs, applies conservative signal QC, and merges adjacent SG4-responsive bins.

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:0030
Reference genome: mm9
Design focus: Region-focused
Region of interest: chr5:118828656-120745441

Perturbation & assay details

pcDNA control or SG4 (Smad1, Smad4, Alk3, and Gata4); no HeLa Wnt response track deposited

The murine BAC library was assayed in HeLa cells as one input DNA, one pcDNA control, and one SG4 sample. GEO deposited normalized BigWig tracks but no thresholded BED call for this pilot. The table uses 50-bp bins across the full murine BAC span, computes log2((SG4 signal + 1)/(pcDNA signal + 1)), calls bins above 0.585, and merges adjacent called bins; these are derived pilot calls, not the paper’s primary COS-7 result set.

Quality control

Because the HeLa pilot has no deposited BED calls, package QC required each 50-bp bin across the Supplementary Table 7 BAC span to have finite mean normalized BigWig signal of at least 75 in input, pcDNA, and SG4 tracks. The 195 bins failing this conservative proxy for the paper’s <75 read-count filter were excluded. Remaining bins were scored with a +1 pseudocount, retained when log2(SG4/pcDNA) >0.585, and merged when adjacent; 910 active bins yielded 236 retained intervals. The single replicate is explicitly marked as exploratory and no replicate-consensus filter was possible.

Curation notes

This HeLa pilot is present in GSE145257 sample metadata but is not described in the main article narrative. It is included as a separate child experiment because the sample set is genuine STARR-seq data, while its lack of a BED call track required transparent derived processing. The target organism denotes the mouse BAC library; HeLa cells are represented by Cellosaurus CVCL:0030. The derived log2 values use normalized BigWig signals and should not be conflated with the primary COS-7 BAM-level comparisons.

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Murine Tbx3/Tbx5 locus STARR-seq HeLa pilot

Processed data

Quality control

Curation notes

Cite OpenMPRA

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