The 58-response-element lentiviral TF-seq library was assayed in wild-type mouse bone-marrow-derived macrophages across a halofuginone dose series with or without 2 mM proline. Samples were collected at 0, 1, and 4 hours after LPS stimulation, with matched control samples and two replicate wells per dose arm.
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
CL:0000235
Reference genome
Not reported / not applicable
Design focus
Synthetic / Motif-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Halofuginone dose series (2.4, 9.7, 39, 156, 625, 2500, or 10000 nM) with or without 2 mM proline; LPS time points at 0, 1, and 4 hours; untreated/control samples
TF-seq used a pooled lentiviral library of 58 synthetic transcription-factor response elements upstream of Luc2P. Each construct had a unique 6-bp response-element tag in the reporter 3' UTR, an 11-nt reporter/integration UMI, and a 10-nt well UMI added during reverse transcription; valid 50-bp single-end reads were collapsed to unique RNA molecules per reporter and well. The dose-response matrix contains halofuginone-only, halofuginone plus 2 mM proline, and control arms at three LPS time points, and retains the minimal-promoter, two negative-control, and technical-spike-in constructs.
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 · 28 definitions
reporter_id
Unique deposited reporter/vector identifier.
pathway
Pathway or response-element label from supplementary Table S1; blank for controls.
transcription_factors
Transcription factor or factor complex represented by the response element.
gene_ids_mouse
Mouse NCBI Gene IDs listed for the response element.
response_element_sequence
Synthetic response-element DNA sequence from supplementary Table S1.
response_element_length_bp
Response-element sequence length in base pairs.
vector_tag_id
Table S1 synthesis/vector tag identifier, when reported.
reporter_tag_sequence
Six-base reporter tag sequence used to identify the construct.
construct_class
Synthetic response element, minimal-promoter control, negative control, or technical spike-in.
supporting_references
Supporting literature URLs cited for the response element.
sample_id
Original time/dose/arm/replicate sample label.
lps_time_hours
Hours after LPS stimulation: 0, 1, or 4.
perturbation
Normalized control, halofuginone-only, or halofuginone plus 2 mM proline condition.
halofuginone_concentration_nM
Halofuginone concentration in nanomolar; zero for source control samples.
proline_mM
Proline concentration in millimolar; 2 for the rescue arm and 0 otherwise.
condition_replicate
Source replicate index within the time/condition grouping; controls have the source control replicate index.
stimulus
LPS stimulus.
raw_rna_umi_count
Unique TF-seq RNA molecules counted for this reporter and sample well.
sample_assay_library_size
Sum of RNA-UMI counts across the 58 Table S1 assay reporters for the sample.
cpm
Reporter count divided by the sample assay library size and multiplied by one million.
log2_cpm
Log2(CPM + 0.5) reporter abundance.
matched_control_baseline_log2_cpm
Mean log2 CPM for the reporter among control samples at the same LPS time point.
log2_fold_change_vs_control
Package-derived log2 CPM contrast versus the matched-time control baseline.
matched_perturbation_log2_cpm
Mean log2 CPM for the reporter in the matched opposite perturbation arm at the same time point and halofuginone dose.
log2_fold_change_vs_matched_perturbation
Package-derived log2 CPM contrast versus the matched opposite perturbation-arm baseline.
detected
True when at least one RNA UMI was observed for the reporter/sample pair.
qc_pass
True when the count is valid and the sample has a positive assay library size.
source_table
Source supplementary table and processing provenance.
Quality control
The authors required a minimum Phred score of 30, an exact match to the constant sequence, and exact valid well and reporter tags before counting unique RNA UMIs; downstream count analysis used edgeR negative-binomial models. Package QC retained rows with numeric non-negative counts and a positive 58-assay-reporter library size. All 61 deposited constructs and 120 sample wells passed these checks; zero counts are retained as valid non-detections. CPM and log2 contrasts in this package are descriptive transformations of the deposited counts and do not add p-values or FDR values.
Curation notes
This table is based on supplementary Table S6. The source uses labels such as T0.9.7nM_Halofuginone; these were parsed as LPS time T0 and dose 9.7 nM. The package includes matched-time control baselines and matched-arm dose contrasts to expose the proline rescue comparison. BMDM cell identity is represented with the Cell Ontology macrophage term CL:0000235. The package-derived contrasts are descriptive and do not replace the paper's edgeR tests or p-values.