HEK293T cells stably transduced with the barcoded Syn1 intron-fragment lentiviral acceptor library were transfected with the splice-donor plasmid. Targeted sequencing of trans-spliced cDNA measures barcode-level activity, with the paired reference-amplicon run providing the DNA denominator.
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
GRCm39
Design focus
Region-focused
Region of interest
chrX:20729970-20730999
Perturbation & assay details
Basal / Untreated
The splice-acceptor library was delivered by a second-generation lentiviral vector and selected as a stable HEK293T population before splice-donor transfection. The public paired reference run is SRR6019583 and the spliced-mRNA run is SRR6019582; both were re-counted at the exact barcode level.
Processed data
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Visible columns (23 of 23)
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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 · 23 definitions
barcode
Unique 20-nt molecular barcode from the splice-acceptor construct.
fragment_id
Identifier for the mapped Syn1 intron 9-10 reference-supported fragment interval.
insert_orientation_relative_to_Syn1
Whether the inserted binding-domain sequence is in Syn1 transcript-sense or reverse-complement orientation.
fragment_start_in_target_transcript_1based
1-based start of the mapped segment in transcript-oriented Syn1 intron 9-10 sequence.
fragment_end_in_target_transcript_1based
1-based end of the mapped segment in transcript-oriented Syn1 intron 9-10 sequence.
genomic_start_GRCm39
1-based GRCm39 genomic start on chrX for the mapped segment.
genomic_end_GRCm39
1-based GRCm39 genomic end on chrX for the mapped segment.
fragment_length
Length in bp of the exact reference-supported mapped segment.
target_sequence_transcript_orientation
Reference sequence for the mapped segment in Syn1 transcript orientation.
fragment_sequence_insert_orientation
Reference sequence in the orientation present in the library insert.
pacbio_library_read_count
Number of valid PacBio CCS library reads carrying this barcode in the lookup extraction.
pacbio_mapping_call_count
Number of PacBio CCS reads contributing an accepted fragment mapping call for this barcode.
pacbio_mapping_agreement
Fraction of accepted PacBio mapping calls supporting the selected orientation.
pacbio_exact_match_length
Length in bp of the best contiguous exact PacBio-to-reference segment used for mapping.
dna_count
Barcode count in the DNA/library reference measurement used as the denominator.
rna_count
Barcode count in the targeted cDNA/RNA splicing measurement.
dna_cpm
DNA count per million normalized over all lookup barcodes with available DNA counts.
rna_cpm
RNA count per million normalized over all lookup barcodes with available RNA counts.
log2_rna_dna
Log2 RNA/DNA activity score using a 0.5 CPM pseudocount.
dna_count_source
Description of the DNA/library measurement used for dna_count.
dna_sra_accession
SRA run accession for the DNA/library measurement, or PacBio lookup source.
rna_sra_accession
SRA run accession for the RNA/splicing measurement.
qc_pass
True for rows retained after the package-level QC filters.
Quality control
The paper's workflow trimmed vector flanks, retained the designed 20-nt V-H-D-B barcode, required unique fragment alignment, and removed PCR template-switching artifacts. For this package, only exact 20-nt ACGT barcodes matching the PacBio CCS lookup and the designed (VHDB)x5 cycle were counted; PacBio mappings required a unique 17-mer seed, an in-range reference-supported exact segment of at least 30 bp, and at least 0.5 orientation-call agreement. Processed rows additionally require dna_count >= 1 and RNA count >= 10. There is one public sequencing run per screen condition, so replicate correlation, dispersion, and FDR filters are not available; failed rows were omitted.
Curation notes
This is the stable-cell version of the paper's second barcode screen. The public archive supplies one reference and one splicing run rather than biological replicate series, so the table reports normalized log2 RNA/DNA scores without p-values or FDR. The generated table contains 694 QC-passing barcode rows; library normalization totals are dna=1183124 and rna=960416.