A retroviral GFP 3′-UTR reporter library containing approximately 27,000 70-nt mouse RBP-occupied and control sequences was transduced into in-vitro differentiated primary mouse Th2 cells. This experiment table represents the Th2 minus PMA/ionomycin condition and reports insert-mediated steady-state mRNA abundance from normalized RNA/DNA ratios.
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:0000546
Reference genome
mm10
Design focus
Region-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Basal / Untreated (in-vitro differentiated mouse Th2 cells; no PMA/ionomycin)
The library was cloned into the 3′ UTR of a murine stem cell virus GFP reporter and delivered by ecotropic retrovirus at MOI <1. Primary CD4+ T cells from C57BL/6J mice were polarized to Th2 cells, cultured for three additional days after transduction, and used for matched genomic-DNA and cDNA amplicon sequencing. Inserts were sequenced as single-end 50-nt reads after amplification with a random hexanucleotide molecular barcode; the published steady_state_mRNA value is the median-normalized RNA/DNA activity score, with values below 1 indicating lower reporter mRNA abundance than the median insert.
Processed data
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Visible columns (19 of 19)
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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 · 19 definitions
element_id
Unique source identifier for the tested fast-UTR library insert (Peakname).
library_subtype
Source sublibrary label; these rows are mouse 3′-UTR GCLiPP peaks.
rapidly_evolving
Source Yes/No flag indicating whether the average mouse-locus PhyloP score is below zero.
locus
70-nt insert locus in the mm10 mouse reference assembly, represented as chromosome:start-end.
gene_symbol
Mouse gene symbol associated with the source 3′-UTR locus.
n_barcodes
Number of unique molecular barcodes recovered for the insert in the source workbook; retained rows have at least two.
total_gdna_reads
Total genomic-DNA sequencing reads assigned to the insert.
normalized_rna_reads
cDNA read abundance normalized so the total cDNA-library read count equals the total genomic-DNA read count.
steady_state_mrna
Median-normalized RNA/DNA ratio used by the authors as the steady-state reporter mRNA abundance/activity score; values below 1 are less stable than the median insert.
Length of sequence in nucleotides; all retained rows are 70.
gc_fraction
Fraction of sequence bases that are G or C.
au_fraction
Fraction of sequence bases that are A or T/U-equivalent in the DNA representation.
mean_phyloP
Mean placental-mammal PhyloP conservation score across the source locus; blank where the source reports NA.
mean_abs_phyloP
Mean absolute PhyloP score across the source locus, a measure of overall evolutionary constraint or acceleration; blank where the source reports NA.
abs_phyloP_minus_phyloP
Source derived feature equal to mean absolute PhyloP minus mean PhyloP; blank where the source reports NA.
folding_energy
Predicted local RNA folding free energy from ViennaRNA RNAfold, in kcal/mol.
icSHAPE_gini_statistic
Gini coefficient of icSHAPE signal used as an in-vivo RNA-structure/folding measure.
Quality control
The authors trimmed vector sequence, aligned reads to the custom oligonucleotide library with Bowtie 2, required each barcode to have at least two genomic-DNA reads, and collapsed barcode-level RNA/DNA ratios only for inserts with at least two independent valid barcodes; they report sequencing more than 95% of the library. The source workbook contains 15,489 nonblank element rows. For this package, 462 rows with N_barcodes=1 were excluded, along with any row lacking a required sequence/activity field or failing the finite-value, 70-nt A/C/G/T, and GC/AU range checks; 15,027 rows passed. No additional total-DNA-read cutoff was imposed because the paper did not specify one.
Curation notes
The processed table is derived from the original Supplemental Table 1 Table 1 sheet, not from raw reads. Although the paper describes four fast-UTR conditions (Th2 and CD8 cells with or without PMA/ionomycin), this deposited workbook explicitly summarizes only the Th2 minus PMA/ionomycin condition; the six linked SRA runs are documented in raw_data/PRJNA516474_SRA_runinfo.csv, and no additional condition-level table is reconstructed. The library is a non-allelic 3′-UTR functional screen, so variant allele columns are not applicable. The workbook has many formatted empty trailing rows; only its 15,489 nonblank element rows were considered before QC. Seven sequence strings are duplicated at distinct source loci and are retained because element IDs and loci remain unique.