A randomly sheared Oregon-R Drosophila melanogaster genomic library containing 4,599,881 approximately 400–500 bp fragments was transiently delivered to S2 cells and assayed under atmospheric normoxia and 0.5% O2 hypoxia. Three biological replicates per condition were quantified through 20N randomer tags in the reporter 5′ UTR; this package retains the 31 published hypoxia-induced enhancer regions that passed the authors’ discovery criteria, with their sequences and annotations.
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
Fruit fly
Taxonomy ID
NCBITaxon:7227
Biosample
CVCL:Z232
Reference genome
dm3
Design focus
Region-focused
Region of interest
Unbiased whole-genome assay (*)
Perturbation & assay details
Hypoxia: 0.5% O2 / 99.5% N2 for 5 h 30 min; comparator atmospheric normoxia
A paired-end library run (SRA SRX468157) linked each genomic fragment to its 20N randomer tag. Activity reads (SRX468694 and SRX468097) were split into three hypoxic and three normoxic biological replicates using inline barcodes. Tags were assigned to the alignment bin and four downstream 100 bp bins, with fractional allocation for tags linked to multiple genomic fragments. Differential activity was tested with a negative-binomial DESeq model; the published table reports the 31 hypoxia-upregulated regions and their hypoxic-versus-normoxic fold changes.
In-vitro-assembled linear reporter MPRA. Randomly sheared Drosophila genomic fragments were placed upstream of a synthetic minimal promoter, intron, 20N randomer tag, EGFP open reading frame, and SV40 terminator; the final linear constructs were transiently transfected with Fugene HD, and reporter RNA randomer tags were sequenced to quantify enhancer activity.
Processed data
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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 · 20 definitions
element_id
Stable package identifier assigned in published statistical-significance order.
source_rank
Rank in Article Table 1, ordered by the published p-value.
genome_coordinate
Normalized dm3 coordinate for the discovered enhancer region, using the paper’s chromosome and interval endpoints.
chromosome
dm3 chromosome name reported by the paper.
start
Published dm3 interval start coordinate.
end
Published dm3 interval end coordinate; the sequence span is end minus start, matching File S3.
fragment_length_bp
Length in base pairs of the File S3 enhancer sequence.
sequence
Drosophila genomic sequence for the identified enhancer region from File S3, written 5′ to 3′ as supplied.
p_value
Published negative-binomial p-value for hypoxic versus normoxic randomer-tag activity.
adjusted_p_value
Published Benjamini–Hochberg adjusted p-value (q-value) for hypoxic versus normoxic activity.
fold_change_hypoxic_vs_normoxic
Published fold change in reporter transcriptional activity under hypoxia relative to normoxia.
log2_fold_change_hypoxic_vs_normoxic
Log2 transform of the published hypoxic-versus-normoxic fold change.
hypoxic_genes_within_20kb
Endogenous hypoxia-upregulated genes reported within 20 kb; ranks and asterisks are retained from Article Table 1.
relative_position_to_hypoxic_gene
Published relative location of the enhancer to the nearby hypoxia-upregulated gene(s).
stress_tf_binding_sites
Stress-response transcription-factor motifs reported in the enhancer by the paper’s motif scan.
proximal_ncRNA
Proximal ncRNA reported in Article Table 2, when available.
ncRNA_position_relative_to_enhancer
Position of the reported ncRNA relative to the enhancer, when available.
ncRNA_hypoxic_read_count
Hypoxic RNA-seq read count for the proximal ncRNA from Article Table 2, when available.
ncRNA_normoxic_read_count
Normoxic RNA-seq read count for the proximal ncRNA from Article Table 2, when available.
source_table
Publication source components used to assemble the row.
Quality control
The authors aligned the paired-end library to dm3 with Bowtie2, generated 100 bp-bin counts from randomer-tag reads, applied an overall-count filter (theta = 0.5), and tested hypoxia versus normoxia with a negative-binomial DESeq model. Published hypoxic enhancers required Benjamini–Hochberg adjusted p-value < 0.1 and p-value < 1.55e-05, with adjacent bins at p-value < 0.05 included in the reported regions. Package QC retained only records present in both Article Table 1 and File S3: finite p-values/q-values in [0,1], fold change > 1, unique dm3 coordinates, DNA sequence containing only A/C/G/T/N, and sequence length exactly matching the published coordinate span. All 31 published enhancer records passed these checks; the table is therefore a significant-region discovery set, not a complete genome-wide count matrix.
Curation notes
This is a single genome-wide region-focused MPRA experiment with paired atmospheric-normoxia and 0.5% O2 hypoxia conditions, not an allele-contrast or variant-focused assay; no rsIDs or alternative alleles were produced. The table integrates the published 31-region MPRA result (Article Table 1) with the matching sequences in File S3 and the three available proximal ncRNA annotations in Article Table 2. File S4 and the analysis code archive remain in raw_data for provenance but are not substituted for the primary hypoxia-versus-normoxia activity table. The paper identifies the cells only as S2 cells supplied by the Ken Prehoda laboratory, so the generic Schneider 2 Cellosaurus mapping CVCL:Z232 is used with that isolate ambiguity noted. SRA accessions: SRX468157 (paired-end fragment-to-randomer matching), SRX468694 and SRX468097 (enhancer activity reads), SRX467593 and SRX467591 (RNA-seq ancillary data); raw reads were not packaged.