A pooled library of previously characterized human ultraconserved noncoding elements was integrated as single-copy Venus reporter constructs in mouse ES cells and then differentiated to Nestin-positive neural progenitors. Fluorescent sorted and unsorted input libraries were sequenced to identify elements enriched for neural-progenitor enhancer activity.
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
Mouse
Taxonomy ID
NCBITaxon:10090
Biosample
CL:0011020
Reference genome
hg38
Design focus
Region-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
In-vitro differentiation to Nestin-positive neural progenitor cells
The pooled ultraconserved-element library used the pSKB1-GW-hsp68-Venus targeting vector, Hprt single-copy integration, FACS enrichment of reporter-positive neural progenitors, and PacBio RS amplicon sequencing. The packaged reference sequences are current VISTA hg38 records linked to the older source UCE identifiers.
Processed data
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Visible columns (26 of 26)
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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 · 26 definitions
element_id
Stable identifier combining VISTA element and source ultraconserved-element ID.
vista_id
VISTA enhancer catalog identifier for the conserved element.
uce_id
Source ultraconserved-element identifier from the Visel 2008 table.
coordinate_assembly
Assembly for the packaged VISTA coordinates.
chromosome
hg38 chromosome.
start
1-based inclusive hg38 start coordinate.
end
1-based inclusive hg38 end coordinate.
element_length_bp
Length of the reported hg38 genomic coordinate interval in base pairs.
source_assay_id
Numbered assay identifier in the source Visel table.
source_test_construct_coordinate_hg17
Test-construct coordinate reported in the older hg17 source table.
source_notes
Notes copied from the source conserved-element table.
input_mapped_reads
QC-passing PacBio read alignments mapped to the element in the unsorted input library.
fluorescent_mapped_reads
QC-passing PacBio read alignments mapped to the element in the fluorescent neural-progenitor library.
input_normalized_read_fraction
Input mapped reads divided by total QC-passing input mapped reads.
fluorescent_normalized_read_fraction
Fluorescent mapped reads divided by total QC-passing fluorescent mapped reads.
log2_enrichment_plus5_pseudocount
Log2 fluorescent-versus-input normalized enrichment with a 5-count pseudocount.
expected_fluorescent_reads
Expected fluorescent count under input-proportional sampling.
derived_poisson_p_value
One-sided Poisson upper-tail p-value using the input-proportional expected fluorescent count; exploratory remapping statistic.
paper_sif_seq_hit
True for the eight elements reported as significantly overrepresented by SIF-seq in the paper.
cns_in_vivo_result
Central-nervous-system result summarized from the paper’s prior E11.5 assay comparison.
prior_e11_5_in_vivo_activity
Prior E11.5 in vivo activity annotation from the source Visel 2008 table.
source_input_run
SRA run accession for the neural-progenitor input library.
source_fluorescent_run
SRA run accession for the fluorescent neural-progenitor library.
source_annotation
Packaged annotation table used to connect VISTA sequences to source IDs and prior annotations.
qc_status
Whether the row passed input-support and read-level QC.
reference_sequence_length_bp
Length of the VISTA reference sequence used for remapping; this can differ from the coordinate span in an API record.
Quality control
Primary PacBio alignments were retained with MAPQ >=20, aligned query length >=100 bp, query aligned fraction >=0.50, and NM-derived estimated identity >=0.70. Only elements with at least one QC-passing input alignment were retained in the table. The paper’s eight reported SIF-seq hits are flagged separately; the exploratory remapped count statistic is not used to relabel hits.
Curation notes
Paired public runs SRR1068176 (input; 36116 QC-passing alignments) and SRR1068177 (fluorescent; 263 QC-passing alignments) were remapped to 231 current VISTA sequences. The table contains 154 input-supported elements; the paper reports 153 successfully tested sites from a 192-element pool and eight significant SIF-seq hits. The small public fluorescent run and updated VISTA references mean these remapped counts are not intended to reproduce the paper figure numerically. Original source annotations use hg17/hg19 conventions, while packaged coordinates are hg38. The VISTA hg38 coordinate span is used for element_length_bp; the fetched reference sequence length is retained separately because hs327 has a sequence/coordinate-length discrepancy in the VISTA API record.