The same episomal primeTF reporter library was profiled in mouse embryonic stem cells after LIF withdrawal for 1, 3, 6, or 24 hours. Reporter activity changes are reported for the 100-TF panel relative to LIF-containing control cells.
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:9108
Reference genome
Not reported / not applicable
Design focus
Synthetic / Motif-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
LIF withdrawal for 1 h, 3 h, 6 h, or 24 h after transfection; control cells remained in LIF-containing 2i medium.
The primeTF reporter plasmid library was transfected into mESCs and reporter RNA barcodes were sequenced. PrimeTF activity was normalized to plasmid DNA and analyzed at each time point; paired chromVAR and TOBIAS values are included for comparison.
Processed data
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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
LIF-containing 2i medium mESC baseline
tested_state
LIF-withdrawal duration represented by the condition
primetime_log2_fc
PrimeTF reporter activity log2 fold change for LIF withdrawal versus control
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. Processed rows were retained only when Dataset EV1 supplied numeric primeTF log2 fold-change and adjusted p-value values; two rows lacking reporter results at the 24 h endpoint were removed. NS is a statistical call, not a QC failure.
Curation notes
The LIF_removal_24h condition is assigned here even though it is also discussed as one of the nine targeted mESC perturbations, preventing duplicate rows across package experiments. The 24 h condition has two source rows without primeTF values; these were excluded rather than imputed.