HTT-locus BAC STARR-seq in BE(2)-C cells
Genome-wide strand asymmetry in massively parallel reporter activity favors genic strandsA pooled library of sheared BAC fragments spanning the HTT locus was assayed in human BE(2)-C neuroblastoma cells using an episomal STARR-seq reporter. Plasmid DNA input and reporter-derived RNA were sequenced in three replicate transfections while retaining fragment orientation relative to the GRCh38 reference.
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
Episomal STARR-seq using 100–500-bp BAC-derived genomic fragments, with a 250–350-bp size-selected library cloned downstream of the super-core promoter in pSTARR-seq_human (Addgene 71509). Three replicate transfections of 40 million BE(2)-C cells with 133 micrograms of pooled reporter plasmid were harvested after 48 hours using FuGENE; paired-end NextSeq reads from plasmid DNA and poly(A)+ reporter RNA were mapped with strand orientation retained. The source GEO signal columns are read-depth-normalized RNA/DNA reporter activities.
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 · 24 definitions
- element_id
- Unique interval identifier formed as chrom:start-end from the GEO binned signal table.
- chrom
- Chromosome name supplied by GEO.
- start
- Source-provided interval start coordinate.
- end
- Source-provided interval end coordinate.
- width
- Width of the source genomic bin in base pairs; 290 for all retained rows.
- source_strand
- Source table strand field; * indicates that the bin itself is not assigned a genomic strand.
- reference_signal_rep1
- Author-supplied normalized RNA/DNA reporter activity for fragments aligned to the GRCh38 Reference strand in replicate 1.
- reference_signal_rep2
- Author-supplied normalized RNA/DNA reporter activity for Reference-strand fragments in replicate 2.
- reference_signal_rep3
- Author-supplied normalized RNA/DNA reporter activity for Reference-strand fragments in replicate 3.
- complement_signal_rep1
- Author-supplied normalized RNA/DNA reporter activity for fragments aligned to the GRCh38 Complement strand in replicate 1.
- complement_signal_rep2
- Author-supplied normalized RNA/DNA reporter activity for Complement-strand fragments in replicate 2.
- complement_signal_rep3
- Author-supplied normalized RNA/DNA reporter activity for Complement-strand fragments in replicate 3.
- reference_signal_mean
- Arithmetic mean of the three Reference-strand reporter-activity replicates.
- complement_signal_mean
- Arithmetic mean of the three Complement-strand reporter-activity replicates.
- reference_signal_sd
- Sample standard deviation across the three Reference-strand reporter-activity replicates.
- complement_signal_sd
- Sample standard deviation across the three Complement-strand reporter-activity replicates.
- rmc_rep1
- Reference signal minus Complement signal for replicate 1.
- rmc_rep2
- Reference signal minus Complement signal for replicate 2.
- rmc_rep3
- Reference signal minus Complement signal for replicate 3.
- rmc_mean
- RMC calculated as mean Reference signal minus mean Complement signal, matching the paper's definition.
- rmc_sd
- Sample standard deviation of the three replicate-specific RMC values.
- mean_strand_signal
- Mean of the Reference and Complement signal means; a strand-averaged reporter activity measure.
- abs_rmc
- Absolute value of rmc_mean.
- qc_pass
- TRUE for rows retained after the GEO source QC flag and finite-value filter.
Quality control
The authors aligned paired-end reads to locus-specific references with Bowtie 2, parsed fragment coordinates and orientation with SAMtools and a custom Perl script, counted Reference and Complement overlaps in 290-bp bins, normalized DNA and RNA counts, and calculated RMC. This package retained only rows with the GEO all_cell_reps_good_data_flag set to TRUE and finite numeric values in all six BE(2)-C strand-signal replicates: 4,278 of 4,829 source bins. No additional arbitrary activity threshold was applied.
Curation notes
The table is a cleaned projection of the author-deposited GSE156857 HTT-locus binned signal table; signal columns are normalized reporter activities rather than raw counts. Coordinates and the source '*' strand field are preserved. The paper text says 14 HTT BACs, whereas Supplemental Table 1 and GEO sample annotations enumerate 13 BAC IDs; the deposited table is used here. The study also reanalyzed external Johnson et al. whole-genome STARR-seq and Van Arensbergen et al. SuRE data, which are linked at the parent level but not duplicated in this compact study package.