HeLa MPRNA screen for lncRNA nuclear-enrichment sequences
High-throughput identification of RNA nuclear enrichment sequencesA pool of 11,969 153-nt oligos densely tiled 38 lncRNA transcripts (mostly 10-nt spacing; 40-nt spacing for kcnq1ot1) was cloned 3' of noncoding fsSox2 and transiently transfected into HeLa. Six biological replicates were fractionated into nuclei and matched total-RNA samples, and barcode RNA-seq quantified nuclear enrichment.
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
Basal / Untreated
Transiently transfected minCMV-fsSox2 reporter plasmid library; each 110-nt lncRNA tile was appended 3' of fsSox2 and paired with a unique 10-nt barcode. After 48 h in HeLa cells, nuclear and matched total-RNA fractions were sequenced by targeted barcode RNA-seq; library-size-normalized oligo counts and modeled nuclear-enrichment differential regions were reported.
Processed data
50 rows per page. Click a cell to inspect its full value.
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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 · 37 definitions
- element_id
- Original unique oligo identifier from GEO, composed of transcript accession, 0-based oligo index, and 10-nt barcode.
- transcript_name
- Human-readable lncRNA/library name from the oligo-pool metadata.
- transcript_accession
- Transcript accession or construct identifier used to match the GEO normalized-count row to the library metadata.
- oligo_index_0based
- 0-based tile index within the transcript/library member.
- barcode_10nt
- Unique 10-nucleotide oligo barcode used for targeted sequencing assignment.
- tile_start_1based
- 1-based inclusive start of the variable RNA tile within the transcript sequence, derived from the library step size.
- tile_end_1based
- 1-based inclusive end of the variable RNA tile within the transcript sequence, derived from oligoGames library metadata.
- tile_length
- Length in nucleotides of the variable RNA tile.
- fish_class
- smFISH localization class recorded for the parental lncRNA in the pool metadata; * denotes unspecified.
- window_step_nt
- Spacing in nucleotides between successive tiled oligos.
- nuclei_rep1_norm_count
- GEO library-size-normalized oligo count for nuclear biological replicate 1.
- nuclei_rep2_norm_count
- GEO library-size-normalized oligo count for nuclear biological replicate 2.
- nuclei_rep3_norm_count
- GEO library-size-normalized oligo count for nuclear biological replicate 3.
- nuclei_rep4_norm_count
- GEO library-size-normalized oligo count for nuclear biological replicate 4.
- nuclei_rep5_norm_count
- GEO library-size-normalized oligo count for nuclear biological replicate 5.
- nuclei_rep6_norm_count
- GEO library-size-normalized oligo count for nuclear biological replicate 6.
- total_rep1_norm_count
- GEO library-size-normalized oligo count for matched total-RNA biological replicate 1.
- total_rep2_norm_count
- GEO library-size-normalized oligo count for matched total-RNA biological replicate 2.
- total_rep3_norm_count
- GEO library-size-normalized oligo count for matched total-RNA biological replicate 3.
- total_rep4_norm_count
- GEO library-size-normalized oligo count for matched total-RNA biological replicate 4.
- total_rep5_norm_count
- GEO library-size-normalized oligo count for matched total-RNA biological replicate 5.
- total_rep6_norm_count
- GEO library-size-normalized oligo count for matched total-RNA biological replicate 6.
- nuclei_mean_norm_count
- Arithmetic mean of the six nuclear normalized counts.
- nuclei_median_norm_count
- Median of the six nuclear normalized counts.
- total_mean_norm_count
- Arithmetic mean of the six matched total-RNA normalized counts.
- total_median_norm_count
- Median of the six matched total-RNA normalized counts.
- median_nuclei_minus_total
- Median across paired replicates of nuclear normalized count minus total-RNA normalized count; positive values indicate greater nuclear signal.
- log2_nuclei_total_ratio_pseudocount_1
- Log2 of (median nuclear normalized count + 1) divided by (median total-RNA normalized count + 1).
- nuclei_detected_reps
- Number of the six nuclear replicates with normalized count greater than zero; used for row-level QC.
- total_detected_reps
- Number of the six total-RNA replicates with normalized count greater than zero; used for row-level QC.
- qc_pass
- TRUE for rows retained after requiring at least 3 detected nuclear and 3 detected total-RNA replicates.
- published_dr_overlap
- TRUE when the derived transcript-local tile interval overlaps one or more of the 109 published differential regions.
- dr_ids
- Local identifiers (DR001-DR109) for overlapping published differential regions, in the order supplied by GEO.
- dr_qvalue_min
- Smallest published Benjamini-Hochberg q-value among overlapping differential regions.
- dr_pvalue_min
- Smallest published empirical p-value among overlapping differential regions.
- dr_statistic_max
- Largest published differential-region summary statistic among overlapping regions.
- dr_coordinates
- Semicolon-separated published differential-region identifiers and transcript-local inclusive coordinates in the form DR###:start-end.
Quality control
The authors required recovery of more than 70% of the oligo pool in each sequencing sample, used an exact 10-nt barcode match with a stringent upstream sequence mismatch filter, and analyzed six biological replicates. For this package, an oligo was retained only when its GEO normalized count was greater than zero in at least 3 of 6 nuclear replicates and at least 3 of 6 total-RNA replicates; 11,132 of 11,969 input oligos (93.01%) passed. The table retains all six replicate values, including zeros, for the retained oligos.
Curation notes
This is the paper's single MPRNA screen, not an allele-contrast enhancer MPRA: the library densely tiles transcript regions and measures RNA nuclear retention. The six Nuclei and six Total columns are the authors' processed biological-replicate labels; GEO sample records also document technical replicate sequencing. Tile coordinates are transcript-local 1-based coordinates derived from oligoMeta.tsv using the authors' oligoGames convention, including the final-oligo endpoint correction. DR annotations use the published chr/start/end intervals and q-values from GSE98828_oligoGames.DRs.tsv.gz; the raw indexStart/indexEnd fields are retained in the source file but were not used for overlap because they are on the authors' modeled index scale. The experiment is performed in human HeLa cells (Cellosaurus CVCL:0030); the pool additionally contains a mouse FIRRE library member (FIRRE(MM)). The processed table contains barcode and tile identity but no oligo sequence string because the authors' GEO normalized-count release does not provide the variable sequences.