MCF-7 RBP-knockdown MPRNA localization and expression
Context-specific effects of sequence elements on subcellular localization of linear and circular RNAsMCF-7 cells were treated with siRNA pools targeting SRSF1, SAFB, IGF2BP1, or IGF2BP2, followed by transfection of the reporter libraries and nuclear/cytoplasmic fractionation. The table reports the authors' median control and knockdown localization/expression scores and knockdown-minus-control localization shifts for spliced, unspliced, and circular reporter contexts.
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.
Perturbation & assay details
10 nM siRNA pool targeting SRSF1, SAFB, IGF2BP1, or IGF2BP2 versus non-targeting control
Cells were transfected with factor-specific siRNA pools, followed 48 h later by NucLibA/CircLibA reporter plasmids and a further 24 h before fractionation. Libraries were measured in total, nuclear, and cytoplasmic RNA. The source final table provides median log2 Nuc/Cyto and whole-cell-extract/plasmid-input values across biological replicates, factor-KD minus non-targeting localization changes, predicted motif counts, and ENCODE eCLIP annotations.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (67 of 67)
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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 · 67 definitions
- element_id
- Unique tested tile identifier from the source finalTab row name.
- library
- Source library label: nucLib for NucLibA or circLib for CircLibA.
- library_index
- Numeric tile index supplied by the source table.
- segment_name
- Author-provided segment name for the tested tile.
- gene_name
- Source gene or noncoding-RNA name from which the tile was derived.
- sequence
- Nucleotide sequence of the tested tile.
- sequence_length
- Length of the tested sequence in nucleotides, calculated from sequence.
- gc_percent
- GC content of the tile in percent, as supplied by the authors.
- delta_g_kcal_mol
- RNAfold-predicted minimum free energy (DeltaG) in kcal/mol, as supplied by the authors.
- srsf1_motif_count
- Number of occurrences of the source SRSF1 motif (CTGGA) in the tile.
- safb_motif_count
- Number of occurrences of the source SAFB motif (GAAAA) in the tile.
- igf2bp1_motif_count
- Number of occurrences of the source IGF2BP1 motif (CCACC) in the tile.
- igf2bp2_motif_count
- Number of occurrences of the source IGF2BP2 motif (CCACC) in the tile.
- srsf1_eclip_encff708ipl
- Per-tile SRSF1 eCLIP annotation/count for ENCODE file ENCFF708IPL, as supplied by the authors.
- srsf1_eclip_encff282dbv
- Per-tile SRSF1 eCLIP annotation/count for ENCODE file ENCFF282DBV, as supplied by the authors.
- srsf1_eclip_encff759ogt
- Per-tile SRSF1 eCLIP annotation/count for ENCODE file ENCFF759OGT, as supplied by the authors.
- srsf1_eclip_encff135sku
- Per-tile SRSF1 eCLIP annotation/count for ENCODE file ENCFF135SKU, as supplied by the authors.
- safb_eclip_encff432svt
- Per-tile SAFB eCLIP annotation/count for ENCODE file ENCFF432SVT, as supplied by the authors.
- safb_eclip_encff024xio
- Per-tile SAFB eCLIP annotation/count for ENCODE file ENCFF024XIO, as supplied by the authors.
- igf2bp1_eclip_encff068fva
- Per-tile IGF2BP1 eCLIP annotation/count for ENCODE file ENCFF068FVA, as supplied by the authors.
- igf2bp1_eclip_encff047wlr
- Per-tile IGF2BP1 eCLIP annotation/count for ENCODE file ENCFF047WLR, as supplied by the authors.
- igf2bp1_eclip_encff228pak
- Per-tile IGF2BP1 eCLIP annotation/count for ENCODE file ENCFF228PAK, as supplied by the authors.
- igf2bp1_eclip_encff324ispliced
- Per-tile IGF2BP1 eCLIP annotation/count for the source ENCFF324ISpliced annotation.
- igf2bp2_eclip_encff205trw
- Per-tile IGF2BP2 eCLIP annotation/count for ENCODE file ENCFF205TRW, as supplied by the authors.
- igf2bp2_eclip_encff922znq
- Per-tile IGF2BP2 eCLIP annotation/count for ENCODE file ENCFF922ZNQ, as supplied by the authors.
- nt_spliced_nuc_cyto_log2_median
- Median log2 Nuc/Cyto ratio across non-targeting-control replicates in the spliced context.
- srsf1_spliced_nuc_cyto_log2_median
- Median log2 Nuc/Cyto ratio across SRSF1-knockdown replicates in the spliced context.
- safb_spliced_nuc_cyto_log2_median
- Median log2 Nuc/Cyto ratio across SAFB-knockdown replicates in the spliced context.
- igf2bp1_spliced_nuc_cyto_log2_median
- Median log2 Nuc/Cyto ratio across IGF2BP1-knockdown replicates in the spliced context.
- igf2bp2_spliced_nuc_cyto_log2_median
- Median log2 Nuc/Cyto ratio across IGF2BP2-knockdown replicates in the spliced context.
- nt_unspliced_nuc_cyto_log2_median
- Median log2 Nuc/Cyto ratio across non-targeting-control replicates in the unspliced context.
- srsf1_unspliced_nuc_cyto_log2_median
- Median log2 Nuc/Cyto ratio across SRSF1-knockdown replicates in the unspliced context.
- safb_unspliced_nuc_cyto_log2_median
- Median log2 Nuc/Cyto ratio across SAFB-knockdown replicates in the unspliced context.
- igf2bp1_unspliced_nuc_cyto_log2_median
- Median log2 Nuc/Cyto ratio across IGF2BP1-knockdown replicates in the unspliced context.
- igf2bp2_unspliced_nuc_cyto_log2_median
- Median log2 Nuc/Cyto ratio across IGF2BP2-knockdown replicates in the unspliced context.
- nt_circular_nuc_cyto_log2_median
- Median log2 Nuc/Cyto ratio across non-targeting-control replicates in the circular context.
- srsf1_circular_nuc_cyto_log2_median
- Median log2 Nuc/Cyto ratio across SRSF1-knockdown replicates in the circular context.
- safb_circular_nuc_cyto_log2_median
- Median log2 Nuc/Cyto ratio across SAFB-knockdown replicates in the circular context.
- igf2bp1_circular_nuc_cyto_log2_median
- Median log2 Nuc/Cyto ratio across IGF2BP1-knockdown replicates in the circular context.
- igf2bp2_circular_nuc_cyto_log2_median
- Median log2 Nuc/Cyto ratio across IGF2BP2-knockdown replicates in the circular context.
- srsf1_minus_nt_spliced_nuc_cyto_log2
- Author-reported median SRSF1-knockdown minus non-targeting change in log2 Nuc/Cyto for spliced reporters.
- safb_minus_nt_spliced_nuc_cyto_log2
- Author-reported median SAFB-knockdown minus non-targeting change in log2 Nuc/Cyto for spliced reporters.
- igf2bp1_minus_nt_spliced_nuc_cyto_log2
- Author-reported median IGF2BP1-knockdown minus non-targeting change in log2 Nuc/Cyto for spliced reporters.
- igf2bp2_minus_nt_spliced_nuc_cyto_log2
- Author-reported median IGF2BP2-knockdown minus non-targeting change in log2 Nuc/Cyto for spliced reporters.
- srsf1_minus_nt_unspliced_nuc_cyto_log2
- Author-reported median SRSF1-knockdown minus non-targeting change in log2 Nuc/Cyto for unspliced reporters.
- safb_minus_nt_unspliced_nuc_cyto_log2
- Author-reported median SAFB-knockdown minus non-targeting change in log2 Nuc/Cyto for unspliced reporters.
- igf2bp1_minus_nt_unspliced_nuc_cyto_log2
- Author-reported median IGF2BP1-knockdown minus non-targeting change in log2 Nuc/Cyto for unspliced reporters.
- igf2bp2_minus_nt_unspliced_nuc_cyto_log2
- Author-reported median IGF2BP2-knockdown minus non-targeting change in log2 Nuc/Cyto for unspliced reporters.
- srsf1_minus_nt_circular_nuc_cyto_log2
- Author-reported median SRSF1-knockdown minus non-targeting change in log2 Nuc/Cyto for circular reporters.
- safb_minus_nt_circular_nuc_cyto_log2
- Author-reported median SAFB-knockdown minus non-targeting change in log2 Nuc/Cyto for circular reporters.
- igf2bp1_minus_nt_circular_nuc_cyto_log2
- Author-reported median IGF2BP1-knockdown minus non-targeting change in log2 Nuc/Cyto for circular reporters.
- igf2bp2_minus_nt_circular_nuc_cyto_log2
- Author-reported median IGF2BP2-knockdown minus non-targeting change in log2 Nuc/Cyto for circular reporters.
- expression_nt_spliced_log2_wce_plasmid_median
- Median log2 WCE/plasmid-input expression ratio for non-targeting control in the spliced context.
- expression_srsf1_spliced_log2_wce_plasmid_median
- Median log2 WCE/plasmid-input expression ratio for SRSF1 knockdown in the spliced context.
- expression_safb_spliced_log2_wce_plasmid_median
- Median log2 WCE/plasmid-input expression ratio for SAFB knockdown in the spliced context.
- expression_igf2bp1_spliced_log2_wce_plasmid_median
- Median log2 WCE/plasmid-input expression ratio for IGF2BP1 knockdown in the spliced context.
- expression_igf2bp2_spliced_log2_wce_plasmid_median
- Median log2 WCE/plasmid-input expression ratio for IGF2BP2 knockdown in the spliced context.
- expression_nt_unspliced_log2_wce_plasmid_median
- Median log2 WCE/plasmid-input expression ratio for non-targeting control in the unspliced context.
- expression_srsf1_unspliced_log2_wce_plasmid_median
- Median log2 WCE/plasmid-input expression ratio for SRSF1 knockdown in the unspliced context.
- expression_safb_unspliced_log2_wce_plasmid_median
- Median log2 WCE/plasmid-input expression ratio for SAFB knockdown in the unspliced context.
- expression_igf2bp1_unspliced_log2_wce_plasmid_median
- Median log2 WCE/plasmid-input expression ratio for IGF2BP1 knockdown in the unspliced context.
- expression_igf2bp2_unspliced_log2_wce_plasmid_median
- Median log2 WCE/plasmid-input expression ratio for IGF2BP2 knockdown in the unspliced context.
- expression_nt_circular_log2_wce_plasmid_median
- Median log2 WCE/plasmid-input expression ratio for non-targeting control in the circular context.
- expression_srsf1_circular_log2_wce_plasmid_median
- Median log2 WCE/plasmid-input expression ratio for SRSF1 knockdown in the circular context.
- expression_safb_circular_log2_wce_plasmid_median
- Median log2 WCE/plasmid-input expression ratio for SAFB knockdown in the circular context.
- expression_igf2bp1_circular_log2_wce_plasmid_median
- Median log2 WCE/plasmid-input expression ratio for IGF2BP1 knockdown in the circular context.
- expression_igf2bp2_circular_log2_wce_plasmid_median
- Median log2 WCE/plasmid-input expression ratio for IGF2BP2 knockdown in the circular context.
Quality control
The authors used the same adapter/UMI-aware read matching and minimum 20-read fragment filter described for the main MPRNA. For this package, rows were required to have an official nucLib or circLib label, a nonempty sequence, and at least one source control/KD median, KD-minus-control localization shift, or KD expression median. This retained 5,132 rows from the 8,162-row source final table; rows lacking any RBP-perturbation result were excluded. No additional biological effect-size threshold was imposed.
Curation notes
This table is a cleaned projection of the authors' Supplementary Data 3 finalTab_230221. The source provides condition medians and localization shifts rather than replicate-level barcode counts or adjusted P-values for the KD MPRA; blanks identify factor/context combinations without a source estimate and are not zeros. Motif and eCLIP annotations are retained to support interpretation of the perturbation results. The library contains orthologous noncoding-RNA tiles as well as human tiles, so no single reference genome is assigned.