A dual-reporter library of 19,342 sequence-mapped synthetic introns with natural splice sites and randomized internal sequence was integrated as single copies into HILO-RMCE HEK293T A2 cells. Ten biological RNA-seq replicates measured spliced GFP, unspliced GFP, and dTomato barcode counts.
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
Human
Taxonomy ID
NCBITaxon:9606
Biosample
CVCL:0063
Reference genome
Not reported / not applicable
Design focus
Synthetic / Motif-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Basal / Untreated
Each construct placed an intron in the 5′ UTR of an EGFP reporter paired with a dTomato reporter; the intron library used natural splice-site sequences, a nominal 160-nt randomized internal region, and paired H18 barcodes. Reporter cassettes were inserted by Cre-mediated recombination-mediated cassette exchange at the HILO-RMCE landing pad, followed by puromycin selection. The ten RNA-seq replicates comprised five full-library and five bottlenecked-library samples. The supplied IME scores are the authors’ DESeq2/Ashr log2 fold-change estimates normalized to four intronless controls.
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 · 50 definitions
element_id
Stable package identifier for the tested element.
barcode
Trusted reporter barcode associated with the intron sequence.
intron_sequence
Full deposited synthetic intron sequence, including constant splice-site flanks.
random_region_sequence
Internal variable sequence after removing the constant splice-site flanks; uppercase DNA.
intron_length
Length of the full deposited intron sequence in nucleotides.
random_region_length
Length of the variable internal sequence in nucleotides.
polyU3_count
Number of overlapping TTT motifs in the variable region; DNA T corresponds to RNA U.
polyU4_count
Number of overlapping TTTT motifs in the variable region; DNA T corresponds to RNA U.
polyU5_count
Number of overlapping TTTTT motifs in the variable region; DNA T corresponds to RNA U.
random_region_gc_fraction
Fraction of variable-region bases that are G or C.
ime_score_log2fc
Authors' DESeq2/Ashr intron-mediated-enhancement log2 fold-change estimate normalized to intronless controls.
deseq_pval
Author-supplied DESeq significance value from supplementary Table S4; blank where the source is blank.
facs_set
Author-supplied iterative-FACS set label: none, green, or red.
median_splicing_efficiency
Author-supplied median fraction of classified GFP reads that were spliced.
bulk_qc_replicates
Number of the ten bulk samples meeting both minimum-count criteria (dTomato >=10 and total GFP >=10).
gfp_spliced_1
Classified spliced GFP RNA-seq reads in bulk biological replicate 1.
gfp_unspliced_1
Classified unspliced GFP RNA-seq reads in bulk biological replicate 1.
dtom_1
Classified dTomato RNA-seq reads in bulk biological replicate 1, used as the paired reporter normalization channel.
gfp_spliced_2
Classified spliced GFP RNA-seq reads in bulk biological replicate 2.
gfp_unspliced_2
Classified unspliced GFP RNA-seq reads in bulk biological replicate 2.
dtom_2
Classified dTomato RNA-seq reads in bulk biological replicate 2, used as the paired reporter normalization channel.
gfp_spliced_3
Classified spliced GFP RNA-seq reads in bulk biological replicate 3.
gfp_unspliced_3
Classified unspliced GFP RNA-seq reads in bulk biological replicate 3.
dtom_3
Classified dTomato RNA-seq reads in bulk biological replicate 3, used as the paired reporter normalization channel.
gfp_spliced_4
Classified spliced GFP RNA-seq reads in bulk biological replicate 4.
gfp_unspliced_4
Classified unspliced GFP RNA-seq reads in bulk biological replicate 4.
dtom_4
Classified dTomato RNA-seq reads in bulk biological replicate 4, used as the paired reporter normalization channel.
gfp_spliced_5
Classified spliced GFP RNA-seq reads in bulk biological replicate 5.
gfp_unspliced_5
Classified unspliced GFP RNA-seq reads in bulk biological replicate 5.
dtom_5
Classified dTomato RNA-seq reads in bulk biological replicate 5, used as the paired reporter normalization channel.
gfp_spliced_6
Classified spliced GFP RNA-seq reads in bulk biological replicate 6.
gfp_unspliced_6
Classified unspliced GFP RNA-seq reads in bulk biological replicate 6.
dtom_6
Classified dTomato RNA-seq reads in bulk biological replicate 6, used as the paired reporter normalization channel.
gfp_spliced_7
Classified spliced GFP RNA-seq reads in bulk biological replicate 7.
gfp_unspliced_7
Classified unspliced GFP RNA-seq reads in bulk biological replicate 7.
dtom_7
Classified dTomato RNA-seq reads in bulk biological replicate 7, used as the paired reporter normalization channel.
gfp_spliced_8
Classified spliced GFP RNA-seq reads in bulk biological replicate 8.
gfp_unspliced_8
Classified unspliced GFP RNA-seq reads in bulk biological replicate 8.
dtom_8
Classified dTomato RNA-seq reads in bulk biological replicate 8, used as the paired reporter normalization channel.
gfp_spliced_9
Classified spliced GFP RNA-seq reads in bulk biological replicate 9.
gfp_unspliced_9
Classified unspliced GFP RNA-seq reads in bulk biological replicate 9.
dtom_9
Classified dTomato RNA-seq reads in bulk biological replicate 9, used as the paired reporter normalization channel.
gfp_spliced_10
Classified spliced GFP RNA-seq reads in bulk biological replicate 10.
gfp_unspliced_10
Classified unspliced GFP RNA-seq reads in bulk biological replicate 10.
dtom_10
Classified dTomato RNA-seq reads in bulk biological replicate 10, used as the paired reporter normalization channel.
gfp_spliced_total
Sum of classified spliced GFP reads across the ten bulk replicates.
gfp_unspliced_total
Sum of classified unspliced GFP reads across the ten bulk replicates.
gfp_total
Sum of spliced and unspliced GFP reads across the ten bulk replicates.
dtom_total
Sum of classified dTomato reads across the ten bulk replicates.
mean_raw_log2_gfp_dtom_ratio
Mean across replicates of log2((1 + GFP spliced + GFP unspliced) / (1 + dTomato)); a non-normalized diagnostic ratio, not the authors' DESeq2 score.
Quality control
Applied the study's trusted barcode-to-intron mapping threshold (<10% mismatch between paired GFP and dTomato barcodes), retained classified RNA-seq counts, and required dTomato >=10 and GFP (spliced + unspliced) >=10 in at least 3 of the 10 samples. This retained 19,342 of 19,342 sequence-mapped elements; 0 elements failed the mapping/count inclusion steps.
Curation notes
The processed table is sequence-centric and follows the authors’ final S4 trusted barcode/sequence dictionary. The nominal library design is 212 nt, but deposited sequences have some length variation, including one 781-nt outlier; exact sequences and length fields are retained. The four intronless control barcodes and the UbC positive-control barcode are present in the raw count matrix but have no S4 random-intron sequence records, so they are not rows in this table. Raw GEO files contain classified RNA-seq counts, not raw sequencing reads.