697 ATAC-STARR-seq prednisolone time course
Epigenomic profiling of glucocorticoid responses identifies cis-regulatory disruptions impacting steroid resistance in childhood acute lymphoblastic leukemiaA chromatin-accessibility-derived ATAC-STARR-seq library from 697 B-ALL cells was tested in 697 cells under vehicle and prednisolone exposure. The processed table contains BasicSTARRseq-called 500-bp regions passing the study's sample-coverage and p-value filters across 0, 6, and 24 h.
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
Vehicle / Untreated; 10 uM prednisolone for 6 h; 10 uM prednisolone for 24 h
Fast-ATAC transposed DNA from 697 cells was size-selected and cloned into the hSTARR-seq_ORI reporter plasmid (Addgene #99296). The library was electroporated into 697 cells; four bulk transfections were split into vehicle, 6-h, and 24-h treatment populations with n=4 replicates per condition. Poly(A) RNA output was compared with plasmid DNA input using BasicSTARRseq; RNA output libraries were merged and downsampled by condition before calling active regions.
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
- Coordinate-derived identifier for a reported ATAC-STARR-seq region; identical coordinates across conditions share the same element ID.
- cell_line
- Cell line used for the ATAC-derived library and assay.
- source_accession
- GEO GSM accession for the RNA output condition.
- input_library_accession
- GEO GSM accession for the corresponding DNA input library.
- timepoint_hours
- Hours after vehicle or prednisolone treatment (0, 6, or 24).
- perturbation
- Vehicle or prednisolone treatment condition.
- chromosome
- hg19 chromosome or contig.
- start
- Reported BasicSTARRseq start coordinate in hg19.
- end
- Reported BasicSTARRseq end coordinate in hg19.
- width
- Reported region width in base pairs (500 for these calls).
- strand
- Reported strand; '*' denotes unstranded.
- sample_coverage
- BasicSTARRseq STARR-seq sample coverage for the region.
- control_coverage
- BasicSTARRseq input-library control coverage for the region.
- p_value
- BasicSTARRseq binomial p-value for STARR-seq enrichment over input.
- enrichment
- BasicSTARRseq normalized STARR-seq-over-input enrichment score.
- log2_enrichment
- Base-2 logarithm of the reported enrichment score, calculated during packaging.
Quality control
The authors mapped reads to hg19 with Bowtie2, called DNA-input peaks with MACS2 at q=0.05, and used BasicSTARRseq to test STARR-seq RNA enrichment over DNA input. Per the supplementary methods, active regions required p<0.001 and sampleCov>=10; the processed table applies both filters and removes all other rows. The deposited GEO CSVs are consolidated outputs for each cell-line/timepoint, so no additional replicate-level filtering was possible from these files.
Curation notes
This table contains 28,122 retained rows: 9,575 at 0 h, 9,503 at 6 h, and 9,044 at 24 h. The library is region-focused and does not provide allele-specific variant contrasts. BasicSTARRseq reports independent fixed-width windows, so the same biological site can have slightly shifted coordinates across conditions. GEO labels the deposited consolidated samples as replicate 1, whereas the paper describes four bulk transfections and n=4 treatment replicates; this package retains the GEO condition-level calls and does not infer replicate-level statistics. Raw sequence reads were intentionally excluded.