Previously unpublished CHO repeat measurement of the Citrine-based alternative 5′ splice-donor reporter library. Approximately 265,000 synthetic members with two 25-nt randomized regions were assayed by targeted RNA sequencing of splice junctions and linked 3′ UTR barcodes.
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
NCBITaxon:10029
Taxonomy ID
NCBITaxon:10029
Biosample
CVCL:0214
Reference genome
Not reported / not applicable
Design focus
Synthetic / Motif-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Basal / Untreated
Episomal Citrine plasmid reporter with two competing 5′ splice donors and a downstream fixed donor; 25 degenerate bases occur downstream of each competing donor. A degenerate 3′ UTR barcode links targeted Illumina HiSeq2000 RNA-seq reads to the originating library member. The processed sd1_psi is donor-1 count divided by all 303 splice-position categories plus the final unspliced/non-splice category, matching the SPLIRENT repository normalizer.
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
Stable generated identifier for the tested library member.
source_row_index
Zero-based row index from Alt_5SS_Tag_to_Seq_Map.csv.
barcode
30-nt sequence tag used to associate RNA reads with the originating plasmid/library member.
sequence
101-bp sequence-map insert containing the fixed splice-donor context and two randomized regions.
sequence_length_bp
Length of sequence in base pairs.
variable_region_1_25nt
First 25-nt randomized region, sequence positions 8–32 (1-based).
variable_region_2_25nt
Second 25-nt randomized region, sequence positions 51–75 (1-based).
qc_pass
True for members retained after the cell-line-specific nonzero total-read filter.
sd1_count
RNA-seq reads assigned to the first fixed 5′ splice donor (matrix column 0; donor 1).
sd2_count
RNA-seq reads assigned to the second fixed 5′ splice donor (matrix column 44).
sd3_count
RNA-seq reads assigned to the downstream fixed donor (matrix column 79).
other_splice_count
Sum of reads in all other splice-position categories (all first 303 matrix columns except SD1, SD2, and SD3).
unspliced_count
Reads in the final matrix category, treated as unspliced/non-splice reads in the repository's isoform denominator.
total_count
Sum of all 303 splice-position categories and the final unspliced/non-splice category.
sd1_psi
Observed donor-1 usage proportion: sd1_count divided by total_count.
sd2_fraction
SD2 reads divided by total_count.
sd3_fraction
SD3 reads divided by total_count.
other_splice_fraction
Other splice-position reads divided by total_count.
unspliced_fraction
Unspliced/non-splice reads divided by total_count.
Quality control
The source archive contains 265,137 library members. Retained the 265,010 members with total mapped assay count >0 in CHO and removed 127 zero-read members. No extra minimum-count cutoff was imposed; this follows the paper/repository nonzero-read QC and preserves the sparse-read measurements.
Curation notes
This is one of the previously unpublished additional cell-line measurements reported in the current paper and is the CHO side of the paper's focused MCF7-versus-CHO differential-splicing analysis. The public multi-cell-line archive also contains HEPG2, LNCAP, and original HEK matrices; those are preserved in raw_data but excluded from the four-cell-line processed study tables. Cellosaurus CVCL:0214 resolves CHO-K1; its species of origin is Cricetulus griseus (NCBITaxon:10029).