An episomal primeTF reporter library probing 100 transcription factors was transfected into mouse embryonic stem cells and profiled after eight unique targeted perturbations. The LIF-removal 24 h endpoint is represented in the separate time-course experiment to avoid duplicating that source condition.
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
UNMAPPED:mouse_embryonic_stem_cell_panel
Reference genome
Not reported / not applicable
Design focus
Synthetic / Motif-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Chiron removal for 24 h; FOXA1 doxycycline induction for 48 h total; 10 uM forskolin for 6 h; 43 C heat shock for 3 h; POU5F1 or SOX2 degradation with 500 nM dTAG-13 for 24 h; 20% FBS serum stimulation for 6 h; or TFCP2L1 knockdown with 40 nM siRNA for 24 h.
The primeTF plasmid library contains optimized synthetic TF reporters with five barcodes per reporter. Reporter RNA barcodes were sequenced after transfection and normalized to plasmid DNA counts with primetime; the paired study also reports chromVAR and TOBIAS ATAC-seq comparisons.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (14 of 14)
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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 · 14 definitions
reporter_tf
Name of the synthetic reporter and assayed transcription factor
condition
Condition label from Dataset EV1
control_state
Baseline state used for the reporter comparison
tested_state
Perturbed state and exposure represented by the condition
primetime_log2_fc
PrimeTF reporter activity log2 fold change for tested versus control state
primetime_adjusted_p_value
Adjusted p-value supplied for the primeTF reporter activity comparison
primetime_significance
Source significance call: Upregulated, Downregulated, or NS
chromvar_difference
Difference in chromVAR TF-associated accessibility score for the paired ATAC-seq comparison
chromvar_adjusted_p_value
Adjusted p-value for the paired chromVAR comparison
chromvar_significance
Source chromVAR significance call
tobias_log2_fc
TOBIAS ATAC-seq TF activity log2 fold change
tobias_p_value
TOBIAS comparison p-value
tobias_significance
Source TOBIAS significance call
qc_status
Row-level package QC status; passed means primeTF effect and adjusted p-value were numeric
Quality control
The paper used primetime v1.0 quality checks for low plasmid-DNA bleedthrough, high barcode correlation, and high biological-replicate correlation. Reporter counts were normalized by sequencing depth and plasmid DNA. Processed rows were retained only when Dataset EV1 supplied numeric primeTF log2 fold-change and adjusted p-value values; 10 rows lacking reporter results were removed from this context. Negative-control reporter rows are preserved in raw primetime outputs but omitted from the TF-focused table. NS is a statistical call, not a QC failure.
Curation notes
This table covers the eight non-time-course conditions in the paper's nine-condition mESC overview. The targeted cell backgrounds were not identical: most conditions used E14TG2a mESCs, SOX2 and POU5F1 degradation used FKBP-tagged degron lines, and FOXA1 overexpression used an inducible cassette line. The paper reports at least two independent biological transfection replicates per condition, with one-replicate limitations for some ATAC comparisons.