The NucLibB AcGFP 3' UTR library was transfected into MCF7 cells after HNRNPK siRNA or non-targeting siRNA treatment. The released source data report per-element knockdown-minus-control differences in nuclear/cytoplasmic, whole-cell-extract/input, nuclear/input, and cytoplasmic/input log2 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
Human
Taxonomy ID
NCBITaxon:9606
Biosample
CVCL:0031
Reference genome
hg19
Design focus
Variant-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
10 nM HNRNPK siRNA pool versus non-targeting siRNA control; 48 h pretreatment followed by NucLibB transfection and 24 h expression
Episomal AcGFP 3' UTR reporter with the NucLibB sequence library. Two HNRNPK-siRNA and two non-targeting-control conditions were analyzed; the released Figure 4H source sheet provides averaged knockdown-minus-control effects. Sequence information was joined from the NucLibB read/count table, and baseline NucLibB annotations were joined where available.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (16 of 16)
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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 · 16 definitions
element_id
Unique NucLibB tile or sequence-variant identifier used in the knockdown source sheet.
sequence
109-nt NucLibB reporter insert sequence recovered from the released NucLibB sequence/count table.
source_gene
Source transcript or ancillary sequence class reported or inferred from the library data.
is_wild_type
Wild-type annotation joined from Supplementary Table 8 when available; blank when unavailable or not reported.
overlaps_repeat
Repeat-overlap annotation joined from Supplementary Table 8 when available; blank when unavailable or not reported.
sirloin_mismatches
Mismatches to the best SIRLOIN match joined from Supplementary Table 8 when available.
sirloin_position
SIRLOIN match position joined from Supplementary Table 8 when available.
best_sirloin_match
Best-matching SIRLOIN sequence joined from Supplementary Table 8 when available.
baseline_nuc_cyt_mean_log2
Mean basal NucLibB nuclear/cytoplasmic log2 ratio from Supplementary Table 8 when available.
baseline_wce_input_mean_log2
Mean basal NucLibB whole-cell-extract/input log2 ratio from Supplementary Table 8 when available.
sirloin_in_kd_analysis
SIRLOIN indicator from the Figure 4H source sheet, coded 1 or 0.
kd_minus_control_nuc_cyt_log2
HNRNPK-knockdown minus non-targeting-control difference in nuclear/cytoplasmic log2 ratio.
kd_minus_control_wce_input_log2
HNRNPK-knockdown minus non-targeting-control difference in whole-cell-extract/input log2 ratio.
kd_minus_control_nuc_input_log2
HNRNPK-knockdown minus non-targeting-control difference in nuclear/input log2 ratio.
kd_minus_control_cyt_input_log2
HNRNPK-knockdown minus non-targeting-control difference in cytoplasmic/input log2 ratio.
qc_pass
true for rows retained because a released Figure 4H knockdown differential and 109-nt sequence were available.
Quality control
The underlying library was processed with the paper's adapter, UMI, quality-aware mismatch, and ambiguous-match rules. The paper reports retaining fragments with at least 10 reads on average in whole-cell-extract samples. For packaging, all elements with a released Figure 4H knockdown differential were retained, and rows without a released Figure 4H record were excluded. All retained records have a 109-nt sequence and at least one non-missing knockdown differential; 30 ancillary records have no matching baseline ratio annotation in Supplementary Table 8 but retain their released knockdown effects.
Curation notes
The processed table contains 1,438 Figure 4H elements. The source sheet uses some names that differ in capitalization or suffixes from the baseline tables; those were matched to the released NucLibB sequence table while preserving the Figure 4H element identifier. Thirty ancillary BORG, FIRRE RRD, and intronic records lack a baseline Supplementary Table 8 annotation, so only their released knockdown effects and sequences are populated.