A pooled 58-response-element lentiviral reporter library was assayed in wild-type and Myd88-knockout mouse bone-marrow-derived macrophages after 12 pathogen-associated molecular patterns at eight time points from 0 to 4 hours. The table contains the reporter RNA-UMI counts for 384 genotype/plate/well conditions, plus the deposited negative and spike-in controls.
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.
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 table also 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 · 25 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 plate/genotype/stimulus/time sample label.
plate
WT1, WT2, KO1, or KO2 source plate/replicate.
genotype
Wild-type or Myd88-knockout BMDM genotype.
replicate
Plate replicate number parsed from the sample label.
stimulus
Canonical name of the PAMP in the sample label; T0 wells are pre-stimulation time-zero wells.
time_hours
Hours after the nominal stimulus time point.
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.
baseline_t0_log2_cpm
Mean log2 CPM across all 24 time-zero wells of the same genotype.
log2_fold_change_vs_t0
Package-derived log2 CPM contrast versus the same-genotype time-zero 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 any reconstruction 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 384 samples passed these checks; zero counts are retained as valid non-detections. Published Table S3 supplied 255 columns because the XLS was limited by Excel's 256-column format; KO1 and KO2 columns were reconstructed from the two public Mendeley FASTQ streams with the authors' parser logic, and KO1 exactly matched all 3,717 overlapping published cells.
Curation notes
BMDMs were generated from pooled bone marrow from two Myd88-knockout and two wild-type littermates; the paper reports n=2 wells per stimulus/time/genotype combination. The raw vectags file labels the TCAGAG and AGCAGT rows as NA; these were resolved to NF.Y and IRF3:IRF7 from Table S1 and the count rows. The package-derived CPM contrasts are descriptive and do not replace the paper's edgeR tests or p-values.