An episomal mutant-tiled STARR-seq library tested 150-bp wild-type oligos and internal-deletion constructs spanning 91 prioritized APOBEC3B regulatory regions plus two negative-control regions. HCT116 cells were assayed after 2 µM gemcitabine treatment in two biological replicates.
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Organism
Human
Taxonomy ID
NCBITaxon:9606
Biosample
CVCL:0291
Reference genome
GRCh38
Design focus
Region-focused
Region of interest
chr22:38699734-39291067
Perturbation & assay details
2 µM gemcitabine
The library was cloned into the hSTARR-seq_ORI episomal reporter (Addgene #99296). The article reports 2,000 wild-type oligos and 8,094 internal-deletion constructs; the distributed Table S6 file contains 2,000 wild-type and 8,093 mutant records, each associated with randomized 15-bp barcodes. The paper used 10-bp RNA UMIs during reverse transcription and added C16 and BX-795 during the post-transfection incubation to limit transfection-induced artifacts. Table S9 reports two biological replicates: HCT116_Gemcitabine2uM_biological_replicate1 and HCT116_Gemcitabine2uM_biological_replicate2.
Processed data
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Column dictionary · 16 definitions
element_id
Base library element identifier shared by the wild-type oligo and its mutant constructs.
oligo_id
Exact STARR-seq construct identifier from Tables S6 and S9.
construct_type
wild_type or internal_deletion_mutant as indicated by the source identifier.
deletion_number
0 for the wild-type construct; source mutant number (1-5) for an internal-deletion construct.
genome_region
GRCh38/hg38 chromosome 22 interval reported for the source oligo.
sequence
150-bp tested insert sequence, without the cloning homology arms.
sequence_length
Length of the tested insert sequence in base pairs.
n_barcodes_rep1
Number of distinct plasmid barcodes assigned to the oligo in biological replicate 1.
n_transcripts_rep1
Number of deduplicated transcript molecules assigned to the oligo in biological replicate 1.
activity_rep1
Authors' normalized expression enrichment for biological replicate 1.
n_barcodes_rep2
Number of distinct plasmid barcodes assigned to the oligo in biological replicate 2.
n_transcripts_rep2
Number of deduplicated transcript molecules assigned to the oligo in biological replicate 2.
activity_rep2
Authors' normalized expression enrichment for biological replicate 2.
activity_mean
Arithmetic mean of the two authors' normalized expression enrichment values.
activity_sd
Sample standard deviation of the two replicate activity values.
log2_activity_mean
Log2 transform of activity_mean, derived for convenient effect-size visualization.
Quality control
Authors discarded plasmid-dictionary reads with mean Illumina Q < 30, deduplicated transcript reads with identical plasmid barcode and RNA UMI, and averaged transcript UMI counts across barcodes per oligo. For this package, 9,643 oligo IDs shared by both biological replicates were retained only when each replicate had at least 5 assigned barcodes and positive transcript counts; 623 oligo IDs failed the barcode criterion and were excluded. No additional activity or significance cutoff was imposed. The retained replicate activity Pearson correlation was 0.658.
Curation notes
HCT116 was obtained from ATCC as CCL-247 and is described in the paper as weakly expressing APOBEC3B. The paper describes this as the gemcitabine STARR-seq activation experiment; Table S9 labels it HCT116_Gemcitabine2uM. The processed table contains 9,020 oligos (1,888 wild type and 7,132 internal-deletion constructs), with a lower retained-row replicate correlation (0.658); no imputation was performed.